HEADER TRANSCRIPTION 29-APR-17 5VNB
TITLE YEATS IN COMPLEX WITH HISTONE H3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: YEATS DOMAIN-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 FRAGMENT: UNP RESIDUES 1-148;
COMPND 5 SYNONYM: GLIOMA-AMPLIFIED SEQUENCE 41,GAS41,NUMA-BINDING PROTEIN 1,
COMPND 6 NUBI1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: H3K23ACK27AC PEPTIDE;
COMPND 10 CHAIN: K;
COMPND 11 ENGINEERED: YES;
COMPND 12 OTHER_DETAILS: HISTONE H3 H3K23ACK27AC PEPTIDE ALY-ACETYLATION
COMPND 13 MODIFICATION ON LYS RESIDUE L-PEPTIDE LINKING
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: YEATS4, GAS41;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGST-PARALLEL;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606
KEYWDS HISTONE READER, YEATS DOMAIN, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR H.J.CHO,T.CIERPICKI
REVDAT 4 15-NOV-23 5VNB 1 REMARK
REVDAT 3 04-OCT-23 5VNB 1 REMARK
REVDAT 2 03-OCT-18 5VNB 1 JRNL
REVDAT 1 05-SEP-18 5VNB 0
JRNL AUTH H.J.CHO,H.LI,B.M.LINHARES,E.KIM,J.NDOJ,H.MIAO,J.GREMBECKA,
JRNL AUTH 2 T.CIERPICKI
JRNL TITL GAS41 RECOGNIZES DIACETYLATED HISTONE H3 THROUGH A BIVALENT
JRNL TITL 2 BINDING MODE.
JRNL REF ACS CHEM. BIOL. V. 13 2739 2018
JRNL REFN ESSN 1554-8937
JRNL PMID 30071723
JRNL DOI 10.1021/ACSCHEMBIO.8B00674
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.67
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 3 NUMBER OF REFLECTIONS : 25753
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) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1354
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) : 2.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1928
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85
REMARK 3 BIN R VALUE (WORKING SET) : 0.2520
REMARK 3 BIN FREE R VALUE SET COUNT : 88
REMARK 3 BIN FREE R VALUE : 0.3090
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4273
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 52
REMARK 3 SOLVENT ATOMS : 132
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.66
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.03000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.03000
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): 0.344
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.422
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4437 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4156 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6004 ; 1.643 ; 1.956
REMARK 3 BOND ANGLES OTHERS (DEGREES): 9574 ; 0.950 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.011 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 213 ;36.834 ;23.897
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 738 ;15.965 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.853 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 640 ; 0.091 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4866 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1045 ; 0.002 ; 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): 2054 ; 4.919 ; 5.708
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2053 ; 4.916 ; 5.706
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2557 ; 7.393 ; 8.526
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2558 ; 7.392 ; 8.529
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2383 ; 5.038 ; 6.049
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2364 ; 4.905 ; 6.029
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3421 ; 7.390 ; 8.844
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4710 ;10.526 ;44.532
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4687 ;10.537 ;44.524
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 : NULL
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 5VNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-17.
REMARK 100 THE DEPOSITION ID IS D_1000227706.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-AUG-16
REMARK 200 TEMPERATURE (KELVIN) : 110
REMARK 200 PH : 9.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : KOHZU
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27276
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 6.80
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 5VNA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.65
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.36 M AMMONIUM SULFATE, 100 MM CHES
REMARK 280 PH 9.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
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 35.39500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.83150
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.15250
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.83150
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.39500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.15250
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, 3, 4
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8100 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8040 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7800 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350
REMARK 350 BIOMOLECULE: 4
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 880 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8350 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, K
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 1
REMARK 465 PHE A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 4
REMARK 465 MET A 5
REMARK 465 ALA A 6
REMARK 465 GLU A 7
REMARK 465 PHE A 8
REMARK 465 GLY A 9
REMARK 465 PRO A 10
REMARK 465 ASP A 11
REMARK 465 SER A 12
REMARK 465 GLY A 13
REMARK 465 GLY A 14
REMARK 465 ARG A 15
REMARK 465 VAL A 16
REMARK 465 LYS A 17
REMARK 465 GLY A 18
REMARK 465 THR A 148
REMARK 465 MET B 1
REMARK 465 PHE B 2
REMARK 465 LYS B 3
REMARK 465 ARG B 4
REMARK 465 MET B 5
REMARK 465 ALA B 6
REMARK 465 GLU B 7
REMARK 465 PHE B 8
REMARK 465 GLY B 9
REMARK 465 PRO B 10
REMARK 465 ASP B 11
REMARK 465 SER B 12
REMARK 465 GLY B 13
REMARK 465 GLY B 14
REMARK 465 ARG B 15
REMARK 465 VAL B 16
REMARK 465 LYS B 17
REMARK 465 GLY B 18
REMARK 465 VAL B 19
REMARK 465 PRO B 147
REMARK 465 THR B 148
REMARK 465 MET C 1
REMARK 465 PHE C 2
REMARK 465 LYS C 3
REMARK 465 ARG C 4
REMARK 465 MET C 5
REMARK 465 ALA C 6
REMARK 465 GLU C 7
REMARK 465 PHE C 8
REMARK 465 GLY C 9
REMARK 465 PRO C 10
REMARK 465 ASP C 11
REMARK 465 SER C 12
REMARK 465 GLY C 13
REMARK 465 GLY C 14
REMARK 465 ARG C 15
REMARK 465 VAL C 16
REMARK 465 LYS C 17
REMARK 465 GLY C 18
REMARK 465 VAL C 19
REMARK 465 PRO C 147
REMARK 465 THR C 148
REMARK 465 MET D 1
REMARK 465 PHE D 2
REMARK 465 LYS D 3
REMARK 465 ARG D 4
REMARK 465 MET D 5
REMARK 465 ALA D 6
REMARK 465 GLU D 7
REMARK 465 PHE D 8
REMARK 465 GLY D 9
REMARK 465 PRO D 10
REMARK 465 ASP D 11
REMARK 465 SER D 12
REMARK 465 GLY D 13
REMARK 465 GLY D 14
REMARK 465 ARG D 15
REMARK 465 VAL D 16
REMARK 465 LYS D 17
REMARK 465 GLY D 18
REMARK 465 VAL D 19
REMARK 465 MET D 128
REMARK 465 LEU D 129
REMARK 465 GLY D 130
REMARK 465 LYS D 131
REMARK 465 ASP D 146
REMARK 465 PRO D 147
REMARK 465 THR D 148
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 132 CG CD CE NZ
REMARK 470 LYS B 36 CG CD CE NZ
REMARK 470 LYS C 36 CG CD CE NZ
REMARK 470 ARG C 110 CG CD NE CZ NH1 NH2
REMARK 470 LEU C 129 CG CD1 CD2
REMARK 470 LYS C 132 CG CD CE NZ
REMARK 470 LYS D 36 CG CD CE NZ
REMARK 470 GLU D 72 CG CD OE1 OE2
REMARK 470 ARG D 110 CG CD NE CZ NH1 NH2
REMARK 470 LYS D 132 CG CD CE NZ
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 O THR A 82 O HOH A 301 2.15
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 LEU B 129 2.05 -68.95
REMARK 500 ASP C 124 -54.73 -28.09
REMARK 500 LYS C 132 -0.07 64.83
REMARK 500 LEU D 120 -42.52 -132.17
REMARK 500 ALA K 25 -52.95 75.63
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH C 333 DISTANCE = 5.93 ANGSTROMS
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 SO4 B 207
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 205
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 206
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 207
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 208
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues ALY K 23
REMARK 800 through ALA K 24 bound to THR K 22
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ARG K 26 and ALY K
REMARK 800 27
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ALY K 27 and SER K
REMARK 800 28
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5VNA RELATED DB: PDB
DBREF 5VNB A 1 148 UNP O95619 YETS4_HUMAN 1 148
DBREF 5VNB B 1 148 UNP O95619 YETS4_HUMAN 1 148
DBREF 5VNB C 1 148 UNP O95619 YETS4_HUMAN 1 148
DBREF 5VNB D 1 148 UNP O95619 YETS4_HUMAN 1 148
DBREF 5VNB K 21 30 PDB 5VNB 5VNB 21 30
SEQRES 1 A 148 MET PHE LYS ARG MET ALA GLU PHE GLY PRO ASP SER GLY
SEQRES 2 A 148 GLY ARG VAL LYS GLY VAL THR ILE VAL LYS PRO ILE VAL
SEQRES 3 A 148 TYR GLY ASN VAL ALA ARG TYR PHE GLY LYS LYS ARG GLU
SEQRES 4 A 148 GLU ASP GLY HIS THR HIS GLN TRP THR VAL TYR VAL LYS
SEQRES 5 A 148 PRO TYR ARG ASN GLU ASP MET SER ALA TYR VAL LYS LYS
SEQRES 6 A 148 ILE GLN PHE LYS LEU HIS GLU SER TYR GLY ASN PRO LEU
SEQRES 7 A 148 ARG VAL VAL THR LYS PRO PRO TYR GLU ILE THR GLU THR
SEQRES 8 A 148 GLY TRP GLY GLU PHE GLU ILE ILE ILE LYS ILE PHE PHE
SEQRES 9 A 148 ILE ASP PRO ASN GLU ARG PRO VAL THR LEU TYR HIS LEU
SEQRES 10 A 148 LEU LYS LEU PHE GLN SER ASP THR ASN ALA MET LEU GLY
SEQRES 11 A 148 LYS LYS THR VAL VAL SER GLU PHE TYR ASP GLU MET ILE
SEQRES 12 A 148 PHE GLN ASP PRO THR
SEQRES 1 B 148 MET PHE LYS ARG MET ALA GLU PHE GLY PRO ASP SER GLY
SEQRES 2 B 148 GLY ARG VAL LYS GLY VAL THR ILE VAL LYS PRO ILE VAL
SEQRES 3 B 148 TYR GLY ASN VAL ALA ARG TYR PHE GLY LYS LYS ARG GLU
SEQRES 4 B 148 GLU ASP GLY HIS THR HIS GLN TRP THR VAL TYR VAL LYS
SEQRES 5 B 148 PRO TYR ARG ASN GLU ASP MET SER ALA TYR VAL LYS LYS
SEQRES 6 B 148 ILE GLN PHE LYS LEU HIS GLU SER TYR GLY ASN PRO LEU
SEQRES 7 B 148 ARG VAL VAL THR LYS PRO PRO TYR GLU ILE THR GLU THR
SEQRES 8 B 148 GLY TRP GLY GLU PHE GLU ILE ILE ILE LYS ILE PHE PHE
SEQRES 9 B 148 ILE ASP PRO ASN GLU ARG PRO VAL THR LEU TYR HIS LEU
SEQRES 10 B 148 LEU LYS LEU PHE GLN SER ASP THR ASN ALA MET LEU GLY
SEQRES 11 B 148 LYS LYS THR VAL VAL SER GLU PHE TYR ASP GLU MET ILE
SEQRES 12 B 148 PHE GLN ASP PRO THR
SEQRES 1 C 148 MET PHE LYS ARG MET ALA GLU PHE GLY PRO ASP SER GLY
SEQRES 2 C 148 GLY ARG VAL LYS GLY VAL THR ILE VAL LYS PRO ILE VAL
SEQRES 3 C 148 TYR GLY ASN VAL ALA ARG TYR PHE GLY LYS LYS ARG GLU
SEQRES 4 C 148 GLU ASP GLY HIS THR HIS GLN TRP THR VAL TYR VAL LYS
SEQRES 5 C 148 PRO TYR ARG ASN GLU ASP MET SER ALA TYR VAL LYS LYS
SEQRES 6 C 148 ILE GLN PHE LYS LEU HIS GLU SER TYR GLY ASN PRO LEU
SEQRES 7 C 148 ARG VAL VAL THR LYS PRO PRO TYR GLU ILE THR GLU THR
SEQRES 8 C 148 GLY TRP GLY GLU PHE GLU ILE ILE ILE LYS ILE PHE PHE
SEQRES 9 C 148 ILE ASP PRO ASN GLU ARG PRO VAL THR LEU TYR HIS LEU
SEQRES 10 C 148 LEU LYS LEU PHE GLN SER ASP THR ASN ALA MET LEU GLY
SEQRES 11 C 148 LYS LYS THR VAL VAL SER GLU PHE TYR ASP GLU MET ILE
SEQRES 12 C 148 PHE GLN ASP PRO THR
SEQRES 1 D 148 MET PHE LYS ARG MET ALA GLU PHE GLY PRO ASP SER GLY
SEQRES 2 D 148 GLY ARG VAL LYS GLY VAL THR ILE VAL LYS PRO ILE VAL
SEQRES 3 D 148 TYR GLY ASN VAL ALA ARG TYR PHE GLY LYS LYS ARG GLU
SEQRES 4 D 148 GLU ASP GLY HIS THR HIS GLN TRP THR VAL TYR VAL LYS
SEQRES 5 D 148 PRO TYR ARG ASN GLU ASP MET SER ALA TYR VAL LYS LYS
SEQRES 6 D 148 ILE GLN PHE LYS LEU HIS GLU SER TYR GLY ASN PRO LEU
SEQRES 7 D 148 ARG VAL VAL THR LYS PRO PRO TYR GLU ILE THR GLU THR
SEQRES 8 D 148 GLY TRP GLY GLU PHE GLU ILE ILE ILE LYS ILE PHE PHE
SEQRES 9 D 148 ILE ASP PRO ASN GLU ARG PRO VAL THR LEU TYR HIS LEU
SEQRES 10 D 148 LEU LYS LEU PHE GLN SER ASP THR ASN ALA MET LEU GLY
SEQRES 11 D 148 LYS LYS THR VAL VAL SER GLU PHE TYR ASP GLU MET ILE
SEQRES 12 D 148 PHE GLN ASP PRO THR
SEQRES 1 K 10 ALA THR ALY ALA ALA ARG ALY SER ALA PRO
HET ALY K 23 12
HET ALY K 27 12
HET EDO A 201 4
HET SO4 A 202 5
HET EDO B 201 4
HET EDO B 202 4
HET EDO B 203 4
HET EDO B 204 4
HET EDO B 205 4
HET EDO B 206 4
HET SO4 B 207 4
HET SO4 B 208 5
HET SO4 B 209 5
HET SO4 C 201 5
HETNAM ALY N(6)-ACETYLLYSINE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM SO4 SULFATE ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 5 ALY 2(C8 H16 N2 O3)
FORMUL 6 EDO 7(C2 H6 O2)
FORMUL 7 SO4 5(O4 S 2-)
FORMUL 18 HOH *132(H2 O)
HELIX 1 AA1 SER A 123 LEU A 129 1 7
HELIX 2 AA2 SER B 123 LEU B 129 1 7
HELIX 3 AA3 ASP C 58 ALA C 61 5 4
HELIX 4 AA4 ASP D 58 ALA D 61 5 4
SHEET 1 AA1 4 GLU A 87 GLY A 92 0
SHEET 2 AA1 4 HIS A 45 PRO A 53 -1 N TRP A 47 O GLU A 90
SHEET 3 AA1 4 THR A 20 TYR A 33 -1 N ARG A 32 O GLN A 46
SHEET 4 AA1 4 VAL A 134 GLN A 145 -1 O PHE A 138 N TYR A 27
SHEET 1 AA2 4 LEU A 78 VAL A 81 0
SHEET 2 AA2 4 VAL A 63 LYS A 69 -1 N PHE A 68 O ARG A 79
SHEET 3 AA2 4 GLU A 97 PHE A 104 -1 O ILE A 99 N LYS A 69
SHEET 4 AA2 4 VAL A 112 LEU A 117 -1 O LEU A 114 N ILE A 100
SHEET 1 AA3 4 GLU B 87 GLY B 92 0
SHEET 2 AA3 4 HIS B 45 PRO B 53 -1 N HIS B 45 O GLY B 92
SHEET 3 AA3 4 ILE B 21 TYR B 33 -1 N VAL B 26 O LYS B 52
SHEET 4 AA3 4 THR B 133 PHE B 144 -1 O PHE B 138 N TYR B 27
SHEET 1 AA4 4 LEU B 78 VAL B 81 0
SHEET 2 AA4 4 VAL B 63 LYS B 69 -1 N ILE B 66 O VAL B 81
SHEET 3 AA4 4 GLU B 97 PHE B 104 -1 O LYS B 101 N GLN B 67
SHEET 4 AA4 4 VAL B 112 LEU B 117 -1 O HIS B 116 N ILE B 98
SHEET 1 AA5 4 TYR C 86 GLY C 92 0
SHEET 2 AA5 4 HIS C 45 PRO C 53 -1 N TRP C 47 O GLU C 90
SHEET 3 AA5 4 ILE C 21 TYR C 33 -1 N VAL C 26 O LYS C 52
SHEET 4 AA5 4 THR C 133 PHE C 144 -1 O PHE C 144 N ILE C 21
SHEET 1 AA6 4 LEU C 78 VAL C 81 0
SHEET 2 AA6 4 VAL C 63 LYS C 69 -1 N PHE C 68 O ARG C 79
SHEET 3 AA6 4 GLU C 97 PHE C 104 -1 O ILE C 99 N LYS C 69
SHEET 4 AA6 4 VAL C 112 LEU C 117 -1 O LEU C 114 N ILE C 100
SHEET 1 AA7 4 TYR D 86 GLY D 92 0
SHEET 2 AA7 4 HIS D 45 PRO D 53 -1 N HIS D 45 O GLY D 92
SHEET 3 AA7 4 ILE D 21 TYR D 33 -1 N VAL D 26 O LYS D 52
SHEET 4 AA7 4 THR D 133 PHE D 144 -1 O VAL D 134 N ALA D 31
SHEET 1 AA8 4 LEU D 78 VAL D 81 0
SHEET 2 AA8 4 VAL D 63 LYS D 69 -1 N PHE D 68 O ARG D 79
SHEET 3 AA8 4 GLU D 97 PHE D 104 -1 O ILE D 99 N LYS D 69
SHEET 4 AA8 4 VAL D 112 LEU D 117 -1 O VAL D 112 N ILE D 102
LINK C THR K 22 N ALY K 23 1555 1555 1.33
LINK C ALY K 23 N ALA K 24 1555 1555 1.32
LINK C ARG K 26 N ALY K 27 1555 1555 1.33
LINK C ALY K 27 N SER K 28 1555 1555 1.33
CISPEP 1 PRO A 84 PRO A 85 0 2.23
CISPEP 2 PRO B 84 PRO B 85 0 4.47
CISPEP 3 PRO C 84 PRO C 85 0 -3.27
CISPEP 4 PRO D 84 PRO D 85 0 -2.76
SITE 1 AC1 1 ASN A 126
SITE 1 AC2 2 GLU A 87 GLU C 137
SITE 1 AC3 3 EDO B 203 EDO B 205 EDO B 206
SITE 1 AC4 2 ALA B 127 EDO B 201
SITE 1 AC5 2 ASP B 124 EDO B 206
SITE 1 AC6 3 GLN B 122 EDO B 201 EDO B 206
SITE 1 AC7 5 ASP B 124 ALA B 127 EDO B 201 EDO B 204
SITE 2 AC7 5 EDO B 205
SITE 1 AC8 2 GLU B 87 GLU D 137
SITE 1 AC9 3 TYR B 50 LYS B 52 GLU B 87
SITE 1 AD1 5 LYS A 131 HOH A 303 LYS B 131 LYS B 132
SITE 2 AD1 5 THR B 133
SITE 1 AD2 4 ASN B 126 LYS B 131 LYS C 52 HOH C 320
SITE 1 AD3 13 HIS B 71 SER B 73 TYR B 74 GLY B 92
SITE 2 AD3 13 TRP B 93 GLY B 94 GLU B 95 PHE B 96
SITE 3 AD3 13 HOH B 314 GLU D 97 THR K 22 ALA K 25
SITE 4 AD3 13 ARG K 26
SITE 1 AD4 12 ASN A 108 GLN A 145 GLU B 97 HIS D 71
SITE 2 AD4 12 TYR D 74 GLY D 92 TRP D 93 GLY D 94
SITE 3 AD4 12 GLU D 95 ALA K 24 ALA K 25 SER K 28
SITE 1 AD5 10 ASN A 108 GLN A 145 HIS D 71 TYR D 74
SITE 2 AD5 10 GLY D 92 TRP D 93 GLY D 94 GLU D 95
SITE 3 AD5 10 ARG K 26 ALA K 29
CRYST1 70.790 80.305 121.663 90.00 90.00 90.00 P 21 21 21 16
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 0.014126 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012453 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008219 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
