HEADER OXIDOREDUCTASE 15-SEP-16 5LWB
TITLE CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH S40650A
CAVEAT 5LWB 79H A 814 HAS WRONG CHIRALITY AT ATOM C3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B,LYSINE-SPECIFIC DEMETHYLASE
COMPND 3 5B,LYSINE-SPECIFIC DEMETHYLASE 5B;
COMPND 4 CHAIN: A;
COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31,CT31,HISTONE DEMETHYLASE JARID1B,
COMPND 6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B,PLU-1,RETINOBLASTOMA-
COMPND 7 BINDING PROTEIN 2 HOMOLOG 1,RBP2-H1,CANCER/TESTIS ANTIGEN 31,CT31,
COMPND 8 HISTONE DEMETHYLASE JARID1B,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN
COMPND 9 1B,PLU-1,RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1,RBP2-H1,
COMPND 10 CANCER/TESTIS ANTIGEN 31,CT31,HISTONE DEMETHYLASE JARID1B,
COMPND 11 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B,PLU-1,RETINOBLASTOMA-
COMPND 12 BINDING PROTEIN 2 HOMOLOG 1,RBP2-H1;
COMPND 13 EC: 1.14.11.-,1.14.11.-,1.14.11.-;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: KDM5B, JARID1B, PLU1, RBBP2H1;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 9 EXPRESSION_SYSTEM_CELL: SF9;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE
KEYWDS LYSINE-SPECIFIC DEMETHYLASE 5B, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.SRIKANNATHASAN,Y.V.LE BIHAN,A.SZYKOWSKA,C.JOHANSSON,C.GILEADI,
AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,F.VON DELFT,U.OPPERMANN,K.HUBER
REVDAT 2 13-NOV-24 5LWB 1 REMARK
REVDAT 1 26-OCT-16 5LWB 0
JRNL AUTH V.SRIKANNATHASAN
JRNL TITL CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH S40650A
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.39 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1682
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.18
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 36355
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.184
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.218
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1855
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 71.2116 - 5.6190 1.00 2867 177 0.1774 0.1884
REMARK 3 2 5.6190 - 4.4602 1.00 2717 156 0.1367 0.1521
REMARK 3 3 4.4602 - 3.8964 1.00 2689 149 0.1407 0.1817
REMARK 3 4 3.8964 - 3.5402 1.00 2681 126 0.1634 0.2083
REMARK 3 5 3.5402 - 3.2865 1.00 2635 151 0.1849 0.2287
REMARK 3 6 3.2865 - 3.0927 1.00 2656 129 0.2021 0.2566
REMARK 3 7 3.0927 - 2.9378 1.00 2634 134 0.2087 0.2520
REMARK 3 8 2.9378 - 2.8099 1.00 2591 165 0.2004 0.2596
REMARK 3 9 2.8099 - 2.7017 1.00 2628 138 0.2363 0.3321
REMARK 3 10 2.7017 - 2.6085 1.00 2640 128 0.2582 0.3469
REMARK 3 11 2.6085 - 2.5269 1.00 2595 135 0.2847 0.3234
REMARK 3 12 2.5269 - 2.4547 0.99 2579 128 0.2752 0.3239
REMARK 3 13 2.4547 - 2.3901 1.00 2588 139 0.2957 0.3377
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.400
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.45
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.009 3847
REMARK 3 ANGLE : 1.164 5225
REMARK 3 CHIRALITY : 0.044 553
REMARK 3 PLANARITY : 0.006 693
REMARK 3 DIHEDRAL : 14.637 1412
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 76.6149 66.4268 11.4952
REMARK 3 T TENSOR
REMARK 3 T11: 0.3013 T22: 0.4738
REMARK 3 T33: 0.3428 T12: -0.0277
REMARK 3 T13: 0.0440 T23: -0.0104
REMARK 3 L TENSOR
REMARK 3 L11: 1.9514 L22: 0.3374
REMARK 3 L33: -0.1063 L12: -0.0188
REMARK 3 L13: 0.1090 L23: -0.0422
REMARK 3 S TENSOR
REMARK 3 S11: 0.0306 S12: -0.0085 S13: 0.1082
REMARK 3 S21: -0.0578 S22: -0.0164 S23: -0.0521
REMARK 3 S31: 0.0112 S32: 0.0363 S33: -0.0197
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5LWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-16.
REMARK 100 THE DEPOSITION ID IS D_1200001466.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-SEP-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949
REMARK 200 MONOCHROMATOR : M
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2
REMARK 200 DATA SCALING SOFTWARE : XIA2
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36414
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390
REMARK 200 RESOLUTION RANGE LOW (A) : 75.770
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 19.40
REMARK 200 R MERGE (I) : 0.13700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 18.60
REMARK 200 R MERGE FOR SHELL (I) : 2.33800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 72.03
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.8M POTTASSIUM
REMARK 280 PHOSPHATE- DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.02667
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.51333
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 75.77000
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.25667
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.28333
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.02667
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 50.51333
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.25667
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 75.77000
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.28333
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 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 SER A -1
REMARK 465 LYS A 368
REMARK 465 LEU A 369
REMARK 465 GLY A 370
REMARK 465 GLY A 371
REMARK 465 GLY A 372
REMARK 465 GLY A 373
REMARK 465 ALA A 374
REMARK 465 GLY A 443
REMARK 465 LYS A 444
REMARK 465 SER A 754
REMARK 465 TYR A 755
REMARK 465 ASN A 756
REMARK 465 GLU A 757
REMARK 465 TRP A 758
REMARK 465 ALA A 759
REMARK 465 LEU A 760
REMARK 465 ASN A 761
REMARK 465 VAL A 762
REMARK 465 ASN A 763
REMARK 465 GLU A 764
REMARK 465 ALA A 765
REMARK 465 LEU A 766
REMARK 465 GLU A 767
REMARK 465 ALA A 768
REMARK 465 LYS A 769
REMARK 465 ILE A 770
REMARK 465 ASN A 771
REMARK 465 LYS A 772
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 GLU A 40 CG CD OE1 OE2
REMARK 470 ILE A 87 CD1
REMARK 470 VAL A 99 CG1 CG2
REMARK 470 LYS A 408 CE NZ
REMARK 470 LYS A 432 CG CD CE NZ
REMARK 470 GLU A 433 CG CD OE1 OE2
REMARK 470 GLU A 450 CG CD OE1 OE2
REMARK 470 GLU A 468 CG CD OE1 OE2
REMARK 470 LYS A 535 CE NZ
REMARK 470 LYS A 536 CD CE NZ
REMARK 470 GLN A 545 CG CD OE1 NE2
REMARK 470 ASP A 547 CG OD1 OD2
REMARK 470 LEU A 548 CG CD1 CD2
REMARK 470 LEU A 549 CG CD1 CD2
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 HOH A 1022 O HOH A 1039 2.06
REMARK 500 NH1 ARG A 65 OE2 GLU A 577 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O1 EDO A 806 O1 EDO A 806 9765 2.06
REMARK 500 O2 EDO A 806 O HOH A 1028 9765 2.19
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 CYS A 723 CA - CB - SG ANGL. DEV. = 7.9 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 CYS A 76 126.24 -173.28
REMARK 500 LEU A 90 79.65 -117.37
REMARK 500 LEU A 93 -2.62 79.65
REMARK 500 PHE A 434 102.83 -162.11
REMARK 500 PHE A 493 -9.63 84.57
REMARK 500 HIS A 550 -18.15 171.82
REMARK 500 PHE A 700 -54.99 -149.13
REMARK 500 LEU A 722 -72.56 -94.40
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 LEU A 549 HIS A 550 -126.30
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 MN A 802 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 91 ND2
REMARK 620 2 LEU A 413 O 148.0
REMARK 620 3 THR A 416 O 117.0 81.9
REMARK 620 4 HOH A 969 O 87.3 90.5 143.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 812 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 499 NE2
REMARK 620 2 GLU A 501 OE2 96.6
REMARK 620 3 HIS A 587 NE2 86.7 88.4
REMARK 620 4 79H A 814 N3 87.4 165.8 105.5
REMARK 620 5 HOH A 910 O 85.7 86.5 170.3 80.2
REMARK 620 6 HOH A 928 O 175.0 87.9 95.6 87.7 92.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 801 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 692 SG
REMARK 620 2 CYS A 695 SG 106.5
REMARK 620 3 CYS A 715 SG 120.5 111.2
REMARK 620 4 HIS A 718 ND1 108.7 106.4 102.7
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 803
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 804
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 805
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 806
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 807
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 808
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 809
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 810
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 811
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 812
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 813
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 79H A 814
DBREF 5LWB A 26 369 UNP Q9UGL1 KDM5B_HUMAN 26 101
DBREF 5LWB A 374 753 UNP Q9UGL1 KDM5B_HUMAN 374 753
DBREF 5LWB A 754 772 UNP Q9UGL1 KDM5B_HUMAN 754 772
SEQADV 5LWB SER A -1 UNP Q9UGL1 EXPRESSION TAG
SEQADV 5LWB MET A 0 UNP Q9UGL1 EXPRESSION TAG
SEQADV 5LWB GLY A 370 UNP Q9UGL1 LINKER
SEQADV 5LWB GLY A 371 UNP Q9UGL1 LINKER
SEQADV 5LWB GLY A 372 UNP Q9UGL1 LINKER
SEQADV 5LWB GLY A 373 UNP Q9UGL1 LINKER
SEQRES 1 A 481 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU
SEQRES 2 A 481 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE
SEQRES 3 A 481 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS
SEQRES 4 A 481 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA
SEQRES 5 A 481 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN
SEQRES 6 A 481 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU
SEQRES 7 A 481 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE
SEQRES 8 A 481 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN
SEQRES 9 A 481 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS
SEQRES 10 A 481 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL
SEQRES 11 A 481 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE
SEQRES 12 A 481 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU
SEQRES 13 A 481 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN
SEQRES 14 A 481 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA
SEQRES 15 A 481 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP
SEQRES 16 A 481 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS
SEQRES 17 A 481 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS
SEQRES 18 A 481 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR
SEQRES 19 A 481 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA
SEQRES 20 A 481 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN
SEQRES 21 A 481 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS
SEQRES 22 A 481 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU
SEQRES 23 A 481 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE
SEQRES 24 A 481 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS
SEQRES 25 A 481 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU
SEQRES 26 A 481 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS
SEQRES 27 A 481 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL
SEQRES 28 A 481 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET
SEQRES 29 A 481 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR
SEQRES 30 A 481 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP
SEQRES 31 A 481 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS
SEQRES 32 A 481 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER
SEQRES 33 A 481 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS
SEQRES 34 A 481 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG
SEQRES 35 A 481 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN
SEQRES 36 A 481 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA
SEQRES 37 A 481 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE ASN LYS
HET ZN A 801 1
HET MN A 802 1
HET EDO A 803 4
HET EDO A 804 4
HET EDO A 805 4
HET EDO A 806 4
HET DMS A 807 4
HET DMS A 808 4
HET DMS A 809 4
HET DMS A 810 4
HET DMS A 811 4
HET MN A 812 1
HET MN A 813 1
HET 79H A 814 25
HETNAM ZN ZINC ION
HETNAM MN MANGANESE (II) ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM 79H 5-[1-[2-(DIMETHYLAMINO)ETHYL]PYRAZOL-4-YL]-7-
HETNAM 2 79H OXIDANYLIDENE-6-PROPAN-2-YL-6~{H}-PYRAZOLO[1,5-
HETNAM 3 79H A]PYRIMIDINE-3-CARBONITRILE
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN ZN 2+
FORMUL 3 MN 3(MN 2+)
FORMUL 4 EDO 4(C2 H6 O2)
FORMUL 8 DMS 5(C2 H6 O S)
FORMUL 15 79H C17 H21 N7 O
FORMUL 16 HOH *153(H2 O)
HELIX 1 AA1 SER A 38 ALA A 43 1 6
HELIX 2 AA2 ASP A 44 GLU A 57 1 14
HELIX 3 AA3 LEU A 379 ASN A 395 1 17
HELIX 4 AA4 PRO A 397 VAL A 401 5 5
HELIX 5 AA5 PRO A 402 THR A 416 1 15
HELIX 6 AA6 SER A 448 TYR A 454 1 7
HELIX 7 AA7 ASN A 460 MET A 467 5 8
HELIX 8 AA8 SER A 470 HIS A 474 5 5
HELIX 9 AA9 ILE A 479 LEU A 484 1 6
HELIX 10 AB1 GLU A 501 SER A 505 5 5
HELIX 11 AB2 PRO A 523 TYR A 525 5 3
HELIX 12 AB3 ALA A 526 ALA A 538 1 13
HELIX 13 AB4 PRO A 539 PHE A 542 5 4
HELIX 14 AB5 ASN A 557 HIS A 564 1 8
HELIX 15 AB6 THR A 604 ASP A 606 5 3
HELIX 16 AB7 TRP A 607 HIS A 622 1 16
HELIX 17 AB8 SER A 628 SER A 638 1 11
HELIX 18 AB9 LYS A 639 LEU A 643 5 5
HELIX 19 AC1 ASP A 644 LEU A 672 1 29
HELIX 20 AC2 ASP A 681 LEU A 685 5 5
HELIX 21 AC3 PRO A 686 ARG A 690 5 5
HELIX 22 AC4 HIS A 718 LEU A 722 5 5
HELIX 23 AC5 PRO A 726 TYR A 728 5 3
HELIX 24 AC6 THR A 737 ALA A 752 1 16
SHEET 1 AA1 8 VAL A 34 PHE A 35 0
SHEET 2 AA1 8 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35
SHEET 3 AA1 8 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64
SHEET 4 AA1 8 TYR A 506 GLY A 514 -1 N SER A 507 O THR A 581
SHEET 5 AA1 8 ASN A 595 PHE A 602 -1 O GLU A 598 N TYR A 510
SHEET 6 AA1 8 TRP A 486 GLY A 490 -1 N TRP A 486 O ALA A 599
SHEET 7 AA1 8 THR A 422 ILE A 429 -1 N ASP A 428 O LEU A 487
SHEET 8 AA1 8 ARG A 86 ARG A 89 -1 N GLN A 88 O VAL A 423
SHEET 1 AA2 2 HIS A 82 PHE A 83 0
SHEET 2 AA2 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83
SHEET 1 AA3 2 GLN A 96 THR A 97 0
SHEET 2 AA3 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96
SHEET 1 AA4 4 SER A 495 HIS A 499 0
SHEET 2 AA4 4 HIS A 587 ASN A 591 -1 O GLY A 589 N PHE A 496
SHEET 3 AA4 4 LYS A 517 GLY A 521 -1 N THR A 518 O PHE A 590
SHEET 4 AA4 4 TYR A 569 GLN A 573 -1 O GLN A 573 N LYS A 517
SHEET 1 AA5 3 ASP A 676 ARG A 679 0
SHEET 2 AA5 3 TYR A 730 TYR A 734 1 O LEU A 732 N ASP A 676
SHEET 3 AA5 3 SER A 702 CYS A 706 -1 N ALA A 703 O ARG A 733
SSBOND 1 CYS A 706 CYS A 723 1555 1555 2.10
SSBOND 2 CYS A 708 CYS A 725 1555 1555 2.03
LINK ND2 ASN A 91 MN MN A 802 1555 1555 2.62
LINK O LEU A 413 MN MN A 802 1555 1555 2.65
LINK O THR A 416 MN MN A 802 1555 1555 2.68
LINK NE2 HIS A 499 MN MN A 812 1555 1555 2.17
LINK OE2 GLU A 501 MN MN A 812 1555 1555 2.00
LINK NE2 HIS A 587 MN MN A 812 1555 1555 2.15
LINK SG CYS A 692 ZN ZN A 801 1555 1555 2.23
LINK SG CYS A 695 ZN ZN A 801 1555 1555 2.31
LINK SG CYS A 715 ZN ZN A 801 1555 1555 2.25
LINK ND1 HIS A 718 ZN ZN A 801 1555 1555 2.10
LINK MN MN A 802 O HOH A 969 1555 1555 2.16
LINK MN MN A 812 N3 79H A 814 1555 1555 2.29
LINK MN MN A 812 O HOH A 910 1555 1555 2.07
LINK MN MN A 812 O HOH A 928 1555 1555 2.38
SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718
SITE 1 AC2 6 LEU A 90 ASN A 91 LEU A 413 THR A 416
SITE 2 AC2 6 GLU A 419 HOH A 969
SITE 1 AC3 6 ASP A 630 CYS A 699 PHE A 700 MET A 701
SITE 2 AC3 6 SER A 702 HOH A 913
SITE 1 AC4 3 GLY A 524 ARG A 584 HOH A 990
SITE 1 AC5 5 ARG A 670 VAL A 674 ILE A 675 HOH A 911
SITE 2 AC5 5 HOH A 938
SITE 1 AC6 4 ASP A 387 VAL A 398 HIS A 399 HOH A1028
SITE 1 AC7 7 TRP A 504 GLU A 531 HIS A 617 TYR A 618
SITE 2 AC7 7 LEU A 621 ARG A 623 HOH A 945
SITE 1 AC8 5 TRP A 486 TYR A 488 SER A 507 ASN A 601
SITE 2 AC8 5 HOH A 910
SITE 1 AC9 7 PHE A 83 GLY A 426 ALA A 427 ASP A 428
SITE 2 AC9 7 LEU A 487 VAL A 489 HOH A 988
SITE 1 AD1 6 MET A 0 LEU A 27 ASN A 559 PRO A 743
SITE 2 AD1 6 ASN A 746 ALA A 747
SITE 1 AD2 5 PHE A 74 ALA A 75 GLY A 435 SER A 436
SITE 2 AD2 5 HOH A1017
SITE 1 AD3 6 HIS A 499 GLU A 501 HIS A 587 79H A 814
SITE 2 AD3 6 HOH A 910 HOH A 928
SITE 1 AD4 3 HIS A 622 HIS A 718 HOH A1021
SITE 1 AD5 17 GLN A 88 THR A 97 ARG A 98 TYR A 425
SITE 2 AD5 17 GLY A 426 TYR A 488 SER A 495 PHE A 496
SITE 3 AD5 17 CYS A 497 HIS A 499 ASN A 509 LYS A 517
SITE 4 AD5 17 HIS A 587 ASN A 591 MN A 812 HOH A 910
SITE 5 AD5 17 HOH A 912
CRYST1 142.360 142.360 151.540 90.00 90.00 120.00 P 65 2 2 12
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 0.007024 0.004056 0.000000 0.00000
SCALE2 0.000000 0.008111 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006599 0.00000