HEADER OXIDOREDUCTASE/STRUCTURAL PROTEIN 20-JUL-14 4QXH
TITLE CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE KDM2A-H3K36ME1 WITH NOG
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A;
COMPND 3 CHAIN: A, C;
COMPND 4 FRAGMENT: UNP RESIDUES 36-364;
COMPND 5 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11, F-BOX/LRR-REPEAT
COMPND 6 PROTEIN 11, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A,
COMPND 7 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A;
COMPND 8 EC: 1.14.11.27;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A;
COMPND 12 CHAIN: B, D;
COMPND 13 FRAGMENT: UNP RESIDUES 450-517;
COMPND 14 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11, F-BOX/LRR-REPEAT
COMPND 15 PROTEIN 11, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A,
COMPND 16 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A;
COMPND 17 EC: 1.14.11.27;
COMPND 18 ENGINEERED: YES;
COMPND 19 MOL_ID: 3;
COMPND 20 MOLECULE: HISTONE H3.2;
COMPND 21 CHAIN: E, F;
COMPND 22 FRAGMENT: UNP RESIDUES 30-44;
COMPND 23 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 GENE: KDM2A, FBXL11, JHDM1A, KIAA1004;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 MOL_ID: 2;
SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 11 ORGANISM_COMMON: MOUSE;
SOURCE 12 ORGANISM_TAXID: 10090;
SOURCE 13 GENE: KDM2A, FBXL11, JHDM1A, KIAA1004;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 17 MOL_ID: 3;
SOURCE 18 SYNTHETIC: YES;
SOURCE 19 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 20 ORGANISM_COMMON: MOUSE;
SOURCE 21 ORGANISM_TAXID: 10090;
SOURCE 22 OTHER_DETAILS: MONO-METHYLATED H3 PEPTIDE WAS SYNTHESIZED
KEYWDS CUPIN SUBFAMILY FE(II)/2-OG DIOXYGENASE, JMJC DOMAIN, HISTONE
KEYWDS 2 DEMETHYLASE, OXIDOREDUCTASE-STRUCTURAL PROTEIN COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Z.J.CHENG,D.J.PATEL
REVDAT 1 05-NOV-14 4QXH 0
JRNL AUTH Z.CHENG,P.CHEUNG,A.J.KUO,E.T.YUKL,C.M.WILMOT,O.GOZANI,
JRNL AUTH 2 D.J.PATEL
JRNL TITL A MOLECULAR THREADING MECHANISM UNDERLIES JUMONJI LYSINE
JRNL TITL 2 DEMETHYLASE KDM2A REGULATION OF METHYLATED H3K36.
JRNL REF GENES DEV. V. 28 1758 2014
JRNL REFN ISSN 0890-9369
JRNL PMID 25128496
JRNL DOI 10.1101/GAD.246561.114
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0049
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.43
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1
REMARK 3 NUMBER OF REFLECTIONS : 38547
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) : 0.190
REMARK 3 R VALUE (WORKING SET) : 0.187
REMARK 3 FREE R VALUE : 0.243
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2047
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2875
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.08
REMARK 3 BIN R VALUE (WORKING SET) : 0.3250
REMARK 3 BIN FREE R VALUE SET COUNT : 144
REMARK 3 BIN FREE R VALUE : 0.3680
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6711
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 22
REMARK 3 SOLVENT ATOMS : 397
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.52
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.88000
REMARK 3 B22 (A**2) : 4.17000
REMARK 3 B33 (A**2) : -3.29000
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): 0.366
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.238
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.216
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.356
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6935 ; 0.012 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6480 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9399 ; 1.567 ; 1.954
REMARK 3 BOND ANGLES OTHERS (DEGREES): 14948 ; 0.838 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 821 ; 6.465 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 342 ;36.776 ;24.064
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1202 ;17.472 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;19.169 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1005 ; 0.087 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7764 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1642 ; 0.001 ; 0.020
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): 3272 ; 2.222 ; 3.451
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3271 ; 2.218 ; 3.450
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4081 ; 3.280 ; 5.164
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3663 ; 2.740 ; 3.750
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 4QXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-14.
REMARK 100 THE RCSB ID CODE IS RCSB086636.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JUL-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38547
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 85.430
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.540
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : 0.06400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.90
REMARK 200 R MERGE FOR SHELL (I) : 0.58000
REMARK 200 R SYM FOR SHELL (I) : 0.43500
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: PHASES
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.18
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M CITRATE NA, 20% PEG 3350, PH
REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
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 27.29700
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.53650
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.38050
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.53650
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.29700
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.38050
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: 6540 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17660 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E
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 350
REMARK 350 BIOMOLECULE: 2
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: 6180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17470 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F
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 ARG E 42
REMARK 465 PRO E 43
REMARK 465 ALA F 29
REMARK 465 ARG F 40
REMARK 465 TYR F 41
REMARK 465 ARG F 42
REMARK 465 PRO F 43
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 LEU C 201 CA - CB - CG ANGL. DEV. = 16.6 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 ASP A 90 134.32 -38.53
REMARK 500 GLN A 116 15.66 54.17
REMARK 500 ILE A 119 -169.06 -126.52
REMARK 500 LYS A 252 43.80 -106.81
REMARK 500 ARG A 319 48.96 74.75
REMARK 500 GLU B 483 -83.74 -76.99
REMARK 500 TYR C 49 49.34 -99.80
REMARK 500 ASN C 50 31.02 -96.94
REMARK 500 GLN C 116 3.79 44.83
REMARK 500 LYS C 252 23.94 -78.17
REMARK 500 GLN C 272 126.70 -28.80
REMARK 500 GLU D 483 -76.63 -70.38
REMARK 500 LYS F 37 129.65 -175.78
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A 601 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 OGA A 600 O2
REMARK 620 2 OGA A 600 O2' 77.4
REMARK 620 3 HIS A 212 NE2 156.3 84.1
REMARK 620 4 HIS A 284 NE2 102.6 106.2 96.6
REMARK 620 5 ASP A 214 OD1 99.5 172.1 96.9 81.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI C 601 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 OGA C 600 O2'
REMARK 620 2 ASP C 214 OD1 158.1
REMARK 620 3 HIS C 212 NE2 89.0 109.5
REMARK 620 4 OGA C 600 O2 68.6 92.8 157.5
REMARK 620 5 HOH C 817 O 89.5 103.2 85.8 92.1
REMARK 620 6 HIS C 284 NE2 82.6 85.7 89.6 89.2 170.9
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 600
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA C 600
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 601
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4TN7 RELATED DB: PDB
REMARK 900 RELATED ID: 4QWN RELATED DB: PDB
REMARK 900 RELATED ID: 4QX7 RELATED DB: PDB
REMARK 900 RELATED ID: 4QX8 RELATED DB: PDB
REMARK 900 RELATED ID: 4QXB RELATED DB: PDB
REMARK 900 RELATED ID: 4QXC RELATED DB: PDB
DBREF 4QXH A 36 364 UNP F6YRW4 F6YRW4_MOUSE 36 364
DBREF 4QXH B 450 517 UNP F6YRW4 F6YRW4_MOUSE 450 517
DBREF 4QXH C 36 364 UNP F6YRW4 F6YRW4_MOUSE 36 364
DBREF 4QXH D 450 517 UNP F6YRW4 F6YRW4_MOUSE 450 517
DBREF 4QXH E 29 43 UNP P84228 H32_MOUSE 30 44
DBREF 4QXH F 29 43 UNP P84228 H32_MOUSE 30 44
SEQRES 1 A 329 ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN LYS
SEQRES 2 A 329 TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS ASP
SEQRES 3 A 329 PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG ASP
SEQRES 4 A 329 PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE LYS
SEQRES 5 A 329 MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS MET
SEQRES 6 A 329 CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP VAL
SEQRES 7 A 329 ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN TRP
SEQRES 8 A 329 THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU LYS
SEQRES 9 A 329 LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR ARG
SEQRES 10 A 329 LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP PHE
SEQRES 11 A 329 ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU LYS
SEQRES 12 A 329 GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU MET
SEQRES 13 A 329 GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER VAL
SEQRES 14 A 329 ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY GLY
SEQRES 15 A 329 THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS VAL
SEQRES 16 A 329 PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU LEU
SEQRES 17 A 329 TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP ILE
SEQRES 18 A 329 PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE GLU
SEQRES 19 A 329 LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY TRP
SEQRES 20 A 329 ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL PHE
SEQRES 21 A 329 GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET GLN
SEQRES 22 A 329 LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL PRO
SEQRES 23 A 329 ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS TRP
SEQRES 24 A 329 TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN ARG
SEQRES 25 A 329 SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SER
SEQRES 26 A 329 MET ASP MET GLU
SEQRES 1 B 68 GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU ARG
SEQRES 2 B 68 CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS LYS
SEQRES 3 B 68 LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA LEU
SEQRES 4 B 68 ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SER
SEQRES 5 B 68 SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE VAL
SEQRES 6 B 68 GLN TRP PRO
SEQRES 1 C 329 ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN LYS
SEQRES 2 C 329 TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS ASP
SEQRES 3 C 329 PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG ASP
SEQRES 4 C 329 PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE LYS
SEQRES 5 C 329 MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS MET
SEQRES 6 C 329 CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP VAL
SEQRES 7 C 329 ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN TRP
SEQRES 8 C 329 THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU LYS
SEQRES 9 C 329 LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR ARG
SEQRES 10 C 329 LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP PHE
SEQRES 11 C 329 ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU LYS
SEQRES 12 C 329 GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU MET
SEQRES 13 C 329 GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER VAL
SEQRES 14 C 329 ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY GLY
SEQRES 15 C 329 THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS VAL
SEQRES 16 C 329 PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU LEU
SEQRES 17 C 329 TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP ILE
SEQRES 18 C 329 PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE GLU
SEQRES 19 C 329 LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY TRP
SEQRES 20 C 329 ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL PHE
SEQRES 21 C 329 GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET GLN
SEQRES 22 C 329 LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL PRO
SEQRES 23 C 329 ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS TRP
SEQRES 24 C 329 TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN ARG
SEQRES 25 C 329 SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SER
SEQRES 26 C 329 MET ASP MET GLU
SEQRES 1 D 68 GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU ARG
SEQRES 2 D 68 CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS LYS
SEQRES 3 D 68 LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA LEU
SEQRES 4 D 68 ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SER
SEQRES 5 D 68 SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE VAL
SEQRES 6 D 68 GLN TRP PRO
SEQRES 1 E 15 ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO HIS ARG TYR
SEQRES 2 E 15 ARG PRO
SEQRES 1 F 15 ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO HIS ARG TYR
SEQRES 2 F 15 ARG PRO
MODRES 4QXH MLZ E 36 LYS N-METHYL-LYSINE
MODRES 4QXH MLZ F 36 LYS N-METHYL-LYSINE
HET MLZ E 36 10
HET MLZ F 36 10
HET OGA A 600 10
HET NI A 601 1
HET OGA C 600 10
HET NI C 601 1
HETNAM MLZ N-METHYL-LYSINE
HETNAM OGA N-OXALYLGLYCINE
HETNAM NI NICKEL (II) ION
FORMUL 5 MLZ 2(C7 H16 N2 O2)
FORMUL 7 OGA 2(C4 H5 N O5)
FORMUL 8 NI 2(NI 2+)
FORMUL 11 HOH *397(H2 O)
HELIX 1 1 ASP A 39 THR A 46 1 8
HELIX 2 2 GLU A 58 PHE A 62 5 5
HELIX 3 3 ASN A 63 GLY A 71 1 9
HELIX 4 4 THR A 94 GLY A 103 1 10
HELIX 5 5 MET A 123 THR A 132 1 10
HELIX 6 6 PRO A 133 ARG A 137 5 5
HELIX 7 7 THR A 151 VAL A 157 5 7
HELIX 8 8 PRO A 160 ASP A 167 1 8
HELIX 9 9 ASP A 167 TRP A 173 1 7
HELIX 10 10 PRO A 174 GLN A 181 1 8
HELIX 11 11 ALA A 187 MET A 191 5 5
HELIX 12 12 ASP A 214 THR A 218 5 5
HELIX 13 13 THR A 237 GLY A 251 1 15
HELIX 14 14 PHE A 257 VAL A 262 5 6
HELIX 15 15 ASN A 304 ARG A 319 1 16
HELIX 16 16 PRO A 321 ARG A 325 5 5
HELIX 17 17 PHE A 328 ASN A 346 1 19
HELIX 18 18 THR A 351 MET A 363 1 13
HELIX 19 19 THR B 454 SER B 470 1 17
HELIX 20 20 PRO B 472 CYS B 477 1 6
HELIX 21 21 ASP B 484 ALA B 500 1 17
HELIX 22 22 ASP C 39 THR C 46 1 8
HELIX 23 23 GLU C 58 PHE C 62 5 5
HELIX 24 24 ASN C 63 GLY C 71 1 9
HELIX 25 25 THR C 94 GLY C 103 1 10
HELIX 26 26 MET C 123 THR C 132 1 10
HELIX 27 27 PRO C 133 ARG C 137 5 5
HELIX 28 28 LEU C 153 VAL C 157 5 5
HELIX 29 29 PRO C 160 ASP C 167 1 8
HELIX 30 30 ASP C 167 MET C 172 1 6
HELIX 31 31 PRO C 174 GLN C 181 1 8
HELIX 32 32 ALA C 187 MET C 191 5 5
HELIX 33 33 ASP C 214 THR C 218 5 5
HELIX 34 34 THR C 237 GLY C 251 1 15
HELIX 35 35 PHE C 257 ARG C 261 5 5
HELIX 36 36 ASN C 304 THR C 318 1 15
HELIX 37 37 PRO C 321 ARG C 325 5 5
HELIX 38 38 PHE C 328 ASN C 346 1 19
HELIX 39 39 THR C 351 MET C 363 1 13
HELIX 40 40 THR D 454 LEU D 471 1 18
HELIX 41 41 PRO D 472 CYS D 477 1 6
HELIX 42 42 ASP D 484 ALA D 500 1 17
SHEET 1 A 9 THR A 55 PHE A 56 0
SHEET 2 A 9 LEU A 76 PHE A 78 1 O ILE A 77 N THR A 55
SHEET 3 A 9 THR A 275 ILE A 278 -1 O THR A 275 N PHE A 78
SHEET 4 A 9 SER A 219 GLN A 226 -1 N VAL A 220 O ILE A 278
SHEET 5 A 9 THR A 292 PHE A 299 -1 O PHE A 299 N SER A 219
SHEET 6 A 9 TYR A 199 SER A 203 -1 N TYR A 199 O GLY A 296
SHEET 7 A 9 TYR A 141 GLU A 147 -1 N LEU A 146 O CYS A 200
SHEET 8 A 9 MET A 107 ASP A 112 -1 N MET A 111 O ASN A 142
SHEET 9 A 9 GLY A 118 THR A 122 -1 O ILE A 119 N VAL A 110
SHEET 1 B 4 TYR A 208 HIS A 212 0
SHEET 2 B 4 ILE A 283 TYR A 287 -1 O HIS A 284 N HIS A 212
SHEET 3 B 4 GLY A 228 ILE A 234 -1 N VAL A 230 O TYR A 287
SHEET 4 B 4 GLN A 266 LYS A 271 -1 O ILE A 268 N PHE A 231
SHEET 1 C 9 THR C 55 PHE C 56 0
SHEET 2 C 9 LEU C 76 PHE C 78 1 O ILE C 77 N THR C 55
SHEET 3 C 9 THR C 275 ILE C 278 -1 O THR C 275 N PHE C 78
SHEET 4 C 9 SER C 219 GLN C 226 -1 N TYR C 222 O PHE C 276
SHEET 5 C 9 THR C 292 PHE C 299 -1 O PHE C 295 N HIS C 223
SHEET 6 C 9 TYR C 199 SER C 203 -1 N SER C 203 O THR C 292
SHEET 7 C 9 TYR C 141 GLU C 147 -1 N VAL C 143 O MET C 202
SHEET 8 C 9 MET C 107 ASP C 112 -1 N MET C 111 O ASN C 142
SHEET 9 C 9 GLY C 118 THR C 122 -1 O ILE C 119 N VAL C 110
SHEET 1 D 4 TYR C 208 HIS C 212 0
SHEET 2 D 4 ILE C 283 TYR C 287 -1 O VAL C 286 N THR C 209
SHEET 3 D 4 GLY C 228 ILE C 234 -1 N VAL C 230 O TYR C 287
SHEET 4 D 4 GLN C 266 LYS C 271 -1 O ILE C 268 N PHE C 231
LINK C VAL E 35 N MLZ E 36 1555 1555 1.34
LINK C MLZ E 36 N LYS E 37 1555 1555 1.34
LINK C VAL F 35 N MLZ F 36 1555 1555 1.33
LINK C MLZ F 36 N LYS F 37 1555 1555 1.34
LINK O2 OGA A 600 NI NI A 601 1555 1555 2.11
LINK O2' OGA C 600 NI NI C 601 1555 1555 2.27
LINK OD1 ASP C 214 NI NI C 601 1555 1555 2.28
LINK O2' OGA A 600 NI NI A 601 1555 1555 2.28
LINK NE2 HIS C 212 NI NI C 601 1555 1555 2.29
LINK NE2 HIS A 212 NI NI A 601 1555 1555 2.29
LINK NE2 HIS A 284 NI NI A 601 1555 1555 2.42
LINK OD1 ASP A 214 NI NI A 601 1555 1555 2.44
LINK O2 OGA C 600 NI NI C 601 1555 1555 2.47
LINK NI NI C 601 O HOH C 817 1555 1555 2.54
LINK NE2 HIS C 284 NI NI C 601 1555 1555 2.57
SITE 1 AC1 12 ASN A 142 ILE A 144 LEU A 201 THR A 209
SITE 2 AC1 12 HIS A 212 ASP A 214 TYR A 222 LYS A 229
SITE 3 AC1 12 HIS A 284 NI A 601 HOH A 721 MLZ E 36
SITE 1 AC2 5 HIS A 212 ASP A 214 HIS A 284 OGA A 600
SITE 2 AC2 5 HOH A 843
SITE 1 AC3 12 ASN C 142 ILE C 144 THR C 209 HIS C 212
SITE 2 AC3 12 ASP C 214 VAL C 220 TYR C 222 LYS C 229
SITE 3 AC3 12 HIS C 284 VAL C 286 NI C 601 MLZ F 36
SITE 1 AC4 5 HIS C 212 ASP C 214 HIS C 284 OGA C 600
SITE 2 AC4 5 HOH C 817
CRYST1 54.594 86.761 171.073 90.00 90.00 90.00 P 21 21 21 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 0.018321 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011562 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005852 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
