HEADER TRANSCRIPTION 15-DEC-09 2X0L
TITLE CRYSTAL STRUCTURE OF A NEURO-SPECIFIC SPLICING VARIANT OF HUMAN
TITLE 2 HISTONE LYSINE DEMETHYLASE LSD1.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2,
COMPND 5 BRAF35-HDAC COMPLEX PROTEIN BHC110;
COMPND 6 EC: 1.-.-.-;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: REST COREPRESSOR 1;
COMPND 10 CHAIN: B;
COMPND 11 SYNONYM: PROTEIN COREST, COREPRESSOR COREST;
COMPND 12 ENGINEERED: YES;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: HISTONE H3 PEPTIDE;
COMPND 15 CHAIN: C;
COMPND 16 FRAGMENT: RESIDUES 2-17;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 MOL_ID: 2;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_COMMON: HUMAN;
SOURCE 10 ORGANISM_TAXID: 9606;
SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 16 ORGANISM_COMMON: HUMAN;
SOURCE 17 ORGANISM_TAXID: 9606
KEYWDS REPRESSOR COMPLEX, CHROMATIN REMODELLING, AMINE OXIDASE,
KEYWDS 2 TRANSCRIPTION, HOST-VIRUS INTERACTION, TRANSCRIPTION REGULATION,
KEYWDS 3 PHOSPHOPROTEIN, OXIDOREDUCTASE, NUCLEAR PROTEIN, CHROMATIN
KEYWDS 4 REGULATOR, DEVELOPMENTAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.ZIBETTI,A.ADAMO,C.BINDA,F.FORNERIS,C.VERPELLI,E.GINELLI,A.MATTEVI,
AUTHOR 2 C.SALA,E.BATTAGLIOLI
REVDAT 3 20-DEC-23 2X0L 1 REMARK
REVDAT 2 14-DEC-16 2X0L 1 COMPND SOURCE REMARK VERSN
REVDAT 2 2 1 DBREF SEQADV
REVDAT 1 02-MAR-10 2X0L 0
JRNL AUTH C.ZIBETTI,A.ADAMO,C.BINDA,F.FORNERIS,E.TOFFOLO,C.VERPELLI,
JRNL AUTH 2 E.GINELLI,A.MATTEVI,C.SALA,E.BATTAGLIOLI
JRNL TITL ALTERNATIVE SPLICING OF THE HISTONE DEMETHYLASE LSD1/KDM1
JRNL TITL 2 CONTRIBUTES TO THE MODULATION OF NEURITE MORPHOGENESIS IN
JRNL TITL 3 THE MAMMALIAN NERVOUS SYSTEM.
JRNL REF J.NEUROSCI. V. 30 2521 2010
JRNL REFN ISSN 0270-6474
JRNL PMID 20164337
JRNL DOI 10.1523/JNEUROSCI.5500-09.2010
REMARK 2
REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.4.0078
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 49397
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.213
REMARK 3 R VALUE (WORKING SET) : 0.212
REMARK 3 FREE R VALUE : 0.252
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900
REMARK 3 FREE R VALUE TEST SET COUNT : 960
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3635
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65
REMARK 3 BIN R VALUE (WORKING SET) : 0.3130
REMARK 3 BIN FREE R VALUE SET COUNT : 67
REMARK 3 BIN FREE R VALUE : 0.3210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6438
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 53
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.13
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 4.37000
REMARK 3 B22 (A**2) : -3.03000
REMARK 3 B33 (A**2) : -1.34000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.339
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.819
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6625 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8984 ; 1.571 ; 1.973
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 816 ; 6.895 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;37.450 ;24.415
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1160 ;21.296 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.361 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1007 ; 0.103 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4973 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4082 ; 0.727 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6593 ; 1.396 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2543 ; 1.716 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2391 ; 3.079 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 2X0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-09.
REMARK 100 THE DEPOSITION ID IS D_1290042093.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.98
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49397
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
REMARK 200 RESOLUTION RANGE LOW (A) : 70.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : 0.11300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 2IW5
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 78.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.70
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.84500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.60500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.72500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.84500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.60500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.72500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.84500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.60500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.72500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.84500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.60500
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.72500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 9020 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38130 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.7 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 123
REMARK 465 ASP A 124
REMARK 465 GLU A 125
REMARK 465 SER A 126
REMARK 465 LEU A 127
REMARK 465 ALA A 128
REMARK 465 ASN A 129
REMARK 465 LEU A 130
REMARK 465 SER A 131
REMARK 465 GLU A 132
REMARK 465 ASP A 133
REMARK 465 GLU A 134
REMARK 465 TYR A 135
REMARK 465 TYR A 136
REMARK 465 SER A 137
REMARK 465 GLU A 138
REMARK 465 GLU A 139
REMARK 465 GLU A 140
REMARK 465 ARG A 141
REMARK 465 ASN A 142
REMARK 465 ALA A 143
REMARK 465 LYS A 144
REMARK 465 ALA A 145
REMARK 465 GLU A 146
REMARK 465 LYS A 147
REMARK 465 GLU A 148
REMARK 465 LYS A 149
REMARK 465 LYS A 150
REMARK 465 LEU A 151
REMARK 465 PRO A 152
REMARK 465 PRO A 153
REMARK 465 PRO A 154
REMARK 465 PRO A 155
REMARK 465 PRO A 156
REMARK 465 GLN A 157
REMARK 465 ALA A 158
REMARK 465 PRO A 159
REMARK 465 PRO A 160
REMARK 465 GLU A 161
REMARK 465 GLU A 162
REMARK 465 GLU A 163
REMARK 465 ASN A 164
REMARK 465 GLU A 165
REMARK 465 SER A 166
REMARK 465 GLU A 167
REMARK 465 PRO A 168
REMARK 465 GLU A 169
REMARK 465 GLU A 170
REMARK 465 PRO A 837
REMARK 465 ARG A 838
REMARK 465 GLN A 839
REMARK 465 ALA A 840
REMARK 465 THR A 841
REMARK 465 PRO A 842
REMARK 465 GLY A 843
REMARK 465 VAL A 844
REMARK 465 PRO A 845
REMARK 465 ALA A 846
REMARK 465 GLN A 847
REMARK 465 GLN A 848
REMARK 465 SER A 849
REMARK 465 PRO A 850
REMARK 465 SER A 851
REMARK 465 MET A 852
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OD1 ASN A 660 OG SER A 749 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 PRO A 635 C - N - CA ANGL. DEV. = 10.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 PHE A 196 50.67 -147.20
REMARK 500 ASN A 224 86.03 -164.51
REMARK 500 SER A 244 -71.28 -70.39
REMARK 500 PRO A 274 128.27 -28.91
REMARK 500 SER A 286 47.87 -108.18
REMARK 500 LYS A 322 111.11 168.74
REMARK 500 MET A 332 -29.11 -142.66
REMARK 500 THR A 335 56.15 -90.92
REMARK 500 ASN A 350 74.32 -52.52
REMARK 500 ASN A 366 65.57 -116.20
REMARK 500 ALA A 369 -161.28 -62.15
REMARK 500 LYS A 372 0.42 -51.73
REMARK 500 ASN A 402 36.69 77.67
REMARK 500 GLN A 438 -6.78 -55.58
REMARK 500 SER A 466 -38.31 -130.95
REMARK 500 GLU A 467 -79.30 61.87
REMARK 500 VAL A 468 96.23 -69.83
REMARK 500 TYR A 494 -8.06 -56.18
REMARK 500 LYS A 503 -76.89 -49.36
REMARK 500 GLU A 510 -81.58 -64.19
REMARK 500 ASN A 514 68.84 -107.91
REMARK 500 ALA A 541 58.01 35.37
REMARK 500 THR A 542 146.25 -174.83
REMARK 500 PRO A 543 121.58 -37.07
REMARK 500 ASN A 587 28.98 45.96
REMARK 500 THR A 610 21.64 -76.35
REMARK 500 ASN A 717 34.83 -89.63
REMARK 500 ALA A 729 -75.79 -43.75
REMARK 500 SER A 737 -33.46 -26.09
REMARK 500 ALA A 757 -59.82 -138.28
REMARK 500 SER A 768 -167.44 -105.97
REMARK 500 SER A 785 -74.27 -61.89
REMARK 500 GLN A 791 121.25 -35.37
REMARK 500 ILE A 793 147.27 -21.49
REMARK 500 TYR A 807 45.71 -145.30
REMARK 500 ALA A 809 14.65 49.84
REMARK 500 TYR A 834 -4.16 -51.46
REMARK 500 PRO B 310 173.57 -53.03
REMARK 500 ALA B 326 -19.77 -44.14
REMARK 500 MET B 340 -60.19 -90.80
REMARK 500 GLU B 341 -35.31 -31.99
REMARK 500 LEU B 363 7.01 -67.95
REMARK 500 PRO B 369 22.80 -73.35
REMARK 500 PRO B 373 147.05 -31.52
REMARK 500 ASP B 401 72.01 -67.69
REMARK 500 ASN B 429 61.44 13.00
REMARK 500 ALA B 439 12.47 -60.33
REMARK 500 THR C 11 -35.86 -137.65
REMARK 500 ALA C 15 66.10 -103.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 PRO A 274 THR A 275 -147.23
REMARK 500 SER A 466 GLU A 467 51.74
REMARK 500 PRO A 792 ILE A 793 145.40
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 900
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2UXX RELATED DB: PDB
REMARK 900 HUMAN LSD1 HISTONE DEMETHYLASE-COREST IN COMPLEX WITH AN FAD-
REMARK 900 TRANYLCYPROMINE ADDUCT
REMARK 900 RELATED ID: 2IW5 RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR COREST-DEPENDENT DEMETHYLATION OF NUCLEOSOMES
REMARK 900 BY THE HUMAN LSD1 HISTONE DEMETHYLASE
REMARK 900 RELATED ID: 2V1D RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3
REMARK 900 RECOGNITION
REMARK 900 RELATED ID: 2UXN RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY
REMARK 900 SUICIDE INACTIVATION
REMARK 900 RELATED ID: 2COM RELATED DB: PDB
REMARK 900 THE SOLUTION STRUCTURE OF THE 33RD FIBRONECTIN TYPE IIIDOMAIN OF
REMARK 900 HUMAN TENASCIN- X
REMARK 900 RELATED ID: 2H94 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE-SPECIFICDEMETHYLASE-
REMARK 900 1
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 SPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN
REMARK 999 RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ADDITIONAL (DTVK)
REMARK 999 RESIDUES THAT HAVE BEEN MARKED AS 369A, 369B, 369C, 369D.
DBREF 2X0L A 123 852 UNP O60341 KDM1_HUMAN 123 852
DBREF 2X0L B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440
DBREF 2X0L C 1 16 UNP Q5TEC6 Q5TEC6_HUMAN 2 17
SEQADV 2X0L ASP A 369A UNP O60341 INSERTION
SEQADV 2X0L THR A 369B UNP O60341 INSERTION
SEQADV 2X0L VAL A 369C UNP O60341 INSERTION
SEQADV 2X0L LYS A 369D UNP O60341 INSERTION
SEQADV 2X0L MET C 4 UNP Q5TEC6 LYS 5 ENGINEERED MUTATION
SEQRES 1 A 734 MET ASP GLU SER LEU ALA ASN LEU SER GLU ASP GLU TYR
SEQRES 2 A 734 TYR SER GLU GLU GLU ARG ASN ALA LYS ALA GLU LYS GLU
SEQRES 3 A 734 LYS LYS LEU PRO PRO PRO PRO PRO GLN ALA PRO PRO GLU
SEQRES 4 A 734 GLU GLU ASN GLU SER GLU PRO GLU GLU PRO SER GLY VAL
SEQRES 5 A 734 GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG
SEQRES 6 A 734 MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE
SEQRES 7 A 734 SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE
SEQRES 8 A 734 ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS
SEQRES 9 A 734 ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU
SEQRES 10 A 734 ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL
SEQRES 11 A 734 HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY
SEQRES 12 A 734 ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR
SEQRES 13 A 734 GLY LYS VAL ILE ILE ILE GLY SER GLY VAL SER GLY LEU
SEQRES 14 A 734 ALA ALA ALA ARG GLN LEU GLN SER PHE GLY MET ASP VAL
SEQRES 15 A 734 THR LEU LEU GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL
SEQRES 16 A 734 ALA THR PHE ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY
SEQRES 17 A 734 ALA MET VAL VAL THR GLY LEU GLY GLY ASN PRO MET ALA
SEQRES 18 A 734 VAL VAL SER LYS GLN VAL ASN MET GLU LEU ALA LYS ILE
SEQRES 19 A 734 LYS GLN LYS CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA
SEQRES 20 A 734 ASP THR VAL LYS VAL PRO LYS GLU LYS ASP GLU MET VAL
SEQRES 21 A 734 GLU GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SER TYR
SEQRES 22 A 734 LEU SER HIS GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS
SEQRES 23 A 734 PRO VAL SER LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN
SEQRES 24 A 734 LEU GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS
SEQRES 25 A 734 TRP LYS LYS ILE VAL LYS THR GLN GLU GLU LEU LYS GLU
SEQRES 26 A 734 LEU LEU ASN LYS MET VAL ASN LEU LYS GLU LYS ILE LYS
SEQRES 27 A 734 GLU LEU HIS GLN GLN TYR LYS GLU ALA SER GLU VAL LYS
SEQRES 28 A 734 PRO PRO ARG ASP ILE THR ALA GLU PHE LEU VAL LYS SER
SEQRES 29 A 734 LYS HIS ARG ASP LEU THR ALA LEU CYS LYS GLU TYR ASP
SEQRES 30 A 734 GLU LEU ALA GLU THR GLN GLY LYS LEU GLU GLU LYS LEU
SEQRES 31 A 734 GLN GLU LEU GLU ALA ASN PRO PRO SER ASP VAL TYR LEU
SEQRES 32 A 734 SER SER ARG ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA
SEQRES 33 A 734 ASN LEU GLU PHE ALA ASN ALA THR PRO LEU SER THR LEU
SEQRES 34 A 734 SER LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE
SEQRES 35 A 734 THR GLY SER HIS LEU THR VAL ARG ASN GLY TYR SER CYS
SEQRES 36 A 734 VAL PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU
SEQRES 37 A 734 ASN THR ALA VAL ARG GLN VAL ARG TYR THR ALA SER GLY
SEQRES 38 A 734 CYS GLU VAL ILE ALA VAL ASN THR ARG SER THR SER GLN
SEQRES 39 A 734 THR PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS THR LEU
SEQRES 40 A 734 PRO LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN
SEQRES 41 A 734 PHE VAL PRO PRO LEU PRO GLU TRP LYS THR SER ALA VAL
SEQRES 42 A 734 GLN ARG MET GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU
SEQRES 43 A 734 CYS PHE ASP ARG VAL PHE TRP ASP PRO SER VAL ASN LEU
SEQRES 44 A 734 PHE GLY HIS VAL GLY SER THR THR ALA SER ARG GLY GLU
SEQRES 45 A 734 LEU PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU
SEQRES 46 A 734 LEU ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE MET GLU
SEQRES 47 A 734 ASN ILE SER ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA
SEQRES 48 A 734 ILE LEU LYS GLY ILE PHE GLY SER SER ALA VAL PRO GLN
SEQRES 49 A 734 PRO LYS GLU THR VAL VAL SER ARG TRP ARG ALA ASP PRO
SEQRES 50 A 734 TRP ALA ARG GLY SER TYR SER TYR VAL ALA ALA GLY SER
SEQRES 51 A 734 SER GLY ASN ASP TYR ASP LEU MET ALA GLN PRO ILE THR
SEQRES 52 A 734 PRO GLY PRO SER ILE PRO GLY ALA PRO GLN PRO ILE PRO
SEQRES 53 A 734 ARG LEU PHE PHE ALA GLY GLU HIS THR ILE ARG ASN TYR
SEQRES 54 A 734 PRO ALA THR VAL HIS GLY ALA LEU LEU SER GLY LEU ARG
SEQRES 55 A 734 GLU ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY ALA MET
SEQRES 56 A 734 TYR THR LEU PRO ARG GLN ALA THR PRO GLY VAL PRO ALA
SEQRES 57 A 734 GLN GLN SER PRO SER MET
SEQRES 1 B 133 ARG LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP
SEQRES 2 B 133 VAL GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR
SEQRES 3 B 133 VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS
SEQRES 4 B 133 ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU
SEQRES 5 B 133 LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU
SEQRES 6 B 133 PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR
SEQRES 7 B 133 GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR
SEQRES 8 B 133 GLY ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN
SEQRES 9 B 133 LYS SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR
SEQRES 10 B 133 ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP
SEQRES 11 B 133 GLU ALA GLU
SEQRES 1 C 16 ALA ARG THR MET GLN THR ALA ARG LYS SER THR GLY GLY
SEQRES 2 C 16 LYS ALA PRO
HET FAD A 900 53
HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE
FORMUL 4 FAD C27 H33 N9 O15 P2
HELIX 1 1 GLY A 173 SER A 181 1 9
HELIX 2 2 THR A 189 PHE A 196 1 8
HELIX 3 3 PHE A 196 GLY A 202 1 7
HELIX 4 4 PRO A 203 ASP A 223 1 21
HELIX 5 5 THR A 230 GLN A 237 1 8
HELIX 6 6 ASP A 245 HIS A 259 1 15
HELIX 7 7 GLY A 287 PHE A 300 1 14
HELIX 8 8 ASN A 340 VAL A 349 1 10
HELIX 9 9 GLU A 373 GLN A 395 1 23
HELIX 10 10 SER A 407 ALA A 465 1 59
HELIX 11 11 ASP A 473 GLU A 512 1 40
HELIX 12 12 SER A 522 ASN A 540 1 19
HELIX 13 13 ASP A 555 GLU A 559 5 5
HELIX 14 14 SER A 572 GLU A 580 1 9
HELIX 15 15 PRO A 626 LYS A 631 1 6
HELIX 16 16 PRO A 644 MET A 654 1 11
HELIX 17 17 THR A 684 ARG A 688 5 5
HELIX 18 18 ALA A 708 MET A 715 1 8
HELIX 19 19 GLU A 716 ILE A 718 5 3
HELIX 20 20 SER A 719 GLY A 736 1 18
HELIX 21 21 ASN A 771 GLN A 778 1 8
HELIX 22 22 GLY A 800 ILE A 804 5 5
HELIX 23 23 THR A 810 GLY A 831 1 22
HELIX 24 24 ALA A 832 LEU A 836 5 5
HELIX 25 25 SER B 317 VAL B 324 1 8
HELIX 26 26 THR B 329 LEU B 363 1 35
HELIX 27 27 ILE B 367 ARG B 371 5 5
HELIX 28 28 THR B 384 GLY B 399 1 16
HELIX 29 29 ASP B 401 GLY B 410 1 10
HELIX 30 30 SER B 413 TYR B 424 1 12
HELIX 31 31 ASN B 429 ALA B 439 1 11
HELIX 32 32 ALA C 1 GLN C 5 5 5
SHEET 1 AA 5 ILE A 584 LYS A 585 0
SHEET 2 AA 5 ASP A 303 LEU A 307 1 O LEU A 306 N LYS A 585
SHEET 3 AA 5 LYS A 280 ILE A 284 1 O VAL A 281 N THR A 305
SHEET 4 AA 5 ALA A 620 CYS A 623 1 O ALA A 620 N ILE A 282
SHEET 5 AA 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623
SHEET 1 AB 2 THR A 319 LYS A 322 0
SHEET 2 AB 2 TYR A 325 ASP A 328 -1 O TYR A 325 N LYS A 322
SHEET 1 AC 3 VAL A 333 VAL A 334 0
SHEET 2 AC 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334
SHEET 3 AC 3 LEU A 353 LYS A 355 -1 O ALA A 354 N THR A 566
SHEET 1 AD 2 TYR A 363 GLU A 364 0
SHEET 2 AD 2 VAL A 369C LYS A 369D-1 O VAL A 369C N GLU A 364
SHEET 1 AE 4 SER A 609 CYS A 618 0
SHEET 2 AE 4 GLY A 599 ASN A 606 -1 O CYS A 600 N CYS A 618
SHEET 3 AE 4 THR A 588 THR A 596 -1 O ALA A 589 N VAL A 605
SHEET 4 AE 4 GLN A 638 VAL A 640 1 O GLN A 638 N VAL A 593
SHEET 1 AF 2 GLY A 655 PHE A 656 0
SHEET 2 AF 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655
SHEET 1 AG 5 LEU A 677 GLY A 679 0
SHEET 2 AG 5 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678
SHEET 3 AG 5 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695
SHEET 4 AG 5 ASN A 660 CYS A 665 -1 O ASN A 660 N VAL A 707
SHEET 5 AG 5 GLU A 745 VAL A 748 -1 O GLU A 745 N CYS A 665
CISPEP 1 ALA A 240 PRO A 241 0 -5.29
CISPEP 2 PRO A 470 PRO A 471 0 4.20
CISPEP 3 GLN A 633 PRO A 634 0 10.69
CISPEP 4 VAL A 640 PRO A 641 0 -1.39
SITE 1 AC1 30 GLY A 285 GLY A 287 VAL A 288 SER A 289
SITE 2 AC1 30 LEU A 307 GLU A 308 ALA A 309 ARG A 310
SITE 3 AC1 30 GLY A 314 GLY A 315 ARG A 316 LEU A 329
SITE 4 AC1 30 GLY A 330 ALA A 331 MET A 332 VAL A 333
SITE 5 AC1 30 THR A 588 VAL A 590 THR A 624 LEU A 625
SITE 6 AC1 30 PRO A 626 TRP A 756 SER A 760 TYR A 761
SITE 7 AC1 30 GLY A 800 GLU A 801 ALA A 809 THR A 810
SITE 8 AC1 30 VAL A 811 MET C 4
CRYST1 119.690 181.210 233.450 90.00 90.00 90.00 I 2 2 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.008355 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005518 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004284 0.00000
(ATOM LINES ARE NOT SHOWN.)
END