HEADER PROTEIN BINDING, LIGASE 31-AUG-09 3IVB TITLE STRUCTURES OF SPOP-SUBSTRATE COMPLEXES: INSIGHTS INTO ARCHITECTURES OF TITLE 2 BTB-CUL3 UBIQUITIN LIGASES: SPOPMATH-MACROH2ASBCPEP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECKLE-TYPE POZ PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 28-166; COMPND 5 SYNONYM: HIB HOMOLOG 1, ROADKILL HOMOLOG 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CORE HISTONE MACRO-H2A.1; COMPND 9 CHAIN: M; COMPND 10 SYNONYM: HISTONE MACROH2A1, MH2A1, H2A.Y, H2A/Y, MEDULLOBLASTOMA COMPND 11 ANTIGEN MU-MB-50.205; COMPND 12 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: SPOP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS PROTEIN BINDING/HYDROLASE, NUCLEUS, UBL CONJUGATION PATHWAY, KEYWDS 2 ALTERNATIVE SPLICING, CHROMATIN REGULATOR, CHROMOSOMAL PROTEIN, DNA- KEYWDS 3 BINDING, ISOPEPTIDE BOND, METHYLATION, NUCLEOSOME CORE, KEYWDS 4 PHOSPHOPROTEIN, UBL CONJUGATION, PROTEIN BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.SCHULMAN,D.J.MILLER,M.F.CALABRESE,S.SEYEDIN REVDAT 2 21-FEB-24 3IVB 1 REMARK SEQADV LINK REVDAT 1 20-OCT-09 3IVB 0 JRNL AUTH M.ZHUANG,M.F.CALABRESE,J.LIU,M.B.WADDELL,A.NOURSE,M.HAMMEL, JRNL AUTH 2 D.J.MILLER,H.WALDEN,D.M.DUDA,S.STEVEN,T.HOGGARD,J.W.HARPER, JRNL AUTH 3 K.P.WHITE,B.A.SCHULMAN JRNL TITL STRUCTURE 9 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 15566 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 828 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1070 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.229 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.697 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1232 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1663 ; 1.249 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 155 ; 6.470 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;34.965 ;23.684 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 227 ;14.350 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;20.457 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 183 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 920 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 541 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 844 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 93 ; 0.234 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.189 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.182 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.137 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 4 ; 0.199 ; 0.200 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): 768 ; 1.133 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1204 ; 1.640 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 529 ; 2.984 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 454 ; 3.334 ; 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): 1297 ; 3.034 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 102 ; 4.916 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1205 ; 1.988 ; 3.000 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 3IVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 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) : 0.9794 REMARK 200 MONOCHROMATOR : NULL 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 : 16414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 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 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% PEG3350, 0.1 M TRIS PH 7.6, 50 REMARK 280 MM ZINC ACETATE. CRYOPROTECTION 30% PEG400, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 177.89333 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 88.94667 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 133.42000 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 44.47333 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 222.36667 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 177.89333 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 88.94667 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 44.47333 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 133.42000 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 222.36667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M 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 GLY A 22 REMARK 465 SER A 23 REMARK 465 GLY A 24 REMARK 465 GLY A 25 REMARK 465 SER A 26 REMARK 465 GLY A 27 REMARK 465 SER A 96 REMARK 465 ASP A 166 REMARK 465 LYS M 166 REMARK 465 ALA M 167 REMARK 465 ALA M 179 REMARK 465 ASP M 180 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 28 CG CD CE NZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 GLN A 165 CG CD OE1 NE2 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 LYS A 135 62.11 -113.79 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 THR M 177 PRO M 178 -34.50 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 44 SG REMARK 620 2 GLU A 47 OE2 106.1 REMARK 620 3 HOH A 226 O 117.8 106.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 113 OE1 REMARK 620 2 HOH A 237 O 105.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 12 O REMARK 620 2 GLU A 97 OE1 120.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 5 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 46 OE2 REMARK 620 2 HOH A 218 O 120.4 REMARK 620 3 HOH A 225 O 122.7 93.2 REMARK 620 N 1 2 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 167 DBREF 3IVB A 28 166 UNP O43791 SPOP_HUMAN 28 166 DBREF 3IVB M 166 180 UNP O75367 H2AY_HUMAN 167 181 SEQADV 3IVB GLY A 22 UNP O43791 EXPRESSION TAG SEQADV 3IVB SER A 23 UNP O43791 EXPRESSION TAG SEQADV 3IVB GLY A 24 UNP O43791 EXPRESSION TAG SEQADV 3IVB GLY A 25 UNP O43791 EXPRESSION TAG SEQADV 3IVB SER A 26 UNP O43791 EXPRESSION TAG SEQADV 3IVB GLY A 27 UNP O43791 EXPRESSION TAG SEQRES 1 A 145 GLY SER GLY GLY SER GLY LYS VAL VAL LYS PHE SER TYR SEQRES 2 A 145 MET TRP THR ILE ASN ASN PHE SER PHE CYS ARG GLU GLU SEQRES 3 A 145 MET GLY GLU VAL ILE LYS SER SER THR PHE SER SER GLY SEQRES 4 A 145 ALA ASN ASP LYS LEU LYS TRP CYS LEU ARG VAL ASN PRO SEQRES 5 A 145 LYS GLY LEU ASP GLU GLU SER LYS ASP TYR LEU SER LEU SEQRES 6 A 145 TYR LEU LEU LEU VAL SER CYS PRO LYS SER GLU VAL ARG SEQRES 7 A 145 ALA LYS PHE LYS PHE SER ILE LEU ASN ALA LYS GLY GLU SEQRES 8 A 145 GLU THR LYS ALA MET GLU SER GLN ARG ALA TYR ARG PHE SEQRES 9 A 145 VAL GLN GLY LYS ASP TRP GLY PHE LYS LYS PHE ILE ARG SEQRES 10 A 145 ARG ASP PHE LEU LEU ASP GLU ALA ASN GLY LEU LEU PRO SEQRES 11 A 145 ASP ASP LYS LEU THR LEU PHE CYS GLU VAL SER VAL VAL SEQRES 12 A 145 GLN ASP SEQRES 1 M 15 LYS ALA ALA SER ALA ASP SER THR THR GLU GLY THR PRO SEQRES 2 M 15 ALA ASP HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET ZN A 4 1 HET ZN A 5 1 HET CL A 167 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 3 ZN 5(ZN 2+) FORMUL 8 CL CL 1- FORMUL 9 HOH *96(H2 O) HELIX 1 1 CYS A 44 GLY A 49 1 6 HELIX 2 2 ASP A 77 LYS A 81 5 5 HELIX 3 3 ARG A 139 ASP A 144 1 6 HELIX 4 4 GLU A 145 GLY A 148 5 4 HELIX 5 5 LEU A 150 LYS A 154 5 5 SHEET 1 A 4 VAL A 30 ILE A 38 0 SHEET 2 A 4 LEU A 155 VAL A 163 -1 O LEU A 155 N ILE A 38 SHEET 3 A 4 VAL A 98 LEU A 107 -1 N LYS A 101 O SER A 162 SHEET 4 A 4 GLU A 113 GLU A 118 -1 O MET A 117 N PHE A 104 SHEET 1 B 4 VAL A 30 ILE A 38 0 SHEET 2 B 4 LEU A 155 VAL A 163 -1 O LEU A 155 N ILE A 38 SHEET 3 B 4 VAL A 98 LEU A 107 -1 N LYS A 101 O SER A 162 SHEET 4 B 4 TYR A 123 PHE A 125 -1 O TYR A 123 N ALA A 100 SHEET 1 C 4 ILE A 52 LYS A 53 0 SHEET 2 C 4 TRP A 67 ASN A 72 -1 O VAL A 71 N ILE A 52 SHEET 3 C 4 TYR A 83 LEU A 90 -1 O LEU A 89 N CYS A 68 SHEET 4 C 4 ASP A 130 ARG A 138 -1 O TRP A 131 N LEU A 88 LINK ZN ZN A 1 SG CYS A 44 1555 1555 2.25 LINK ZN ZN A 1 OE2 GLU A 47 1555 1555 2.10 LINK ZN ZN A 1 O HOH A 226 1555 1555 2.14 LINK ZN ZN A 2 OE1 GLU A 113 1555 1555 2.00 LINK ZN ZN A 2 O HOH A 237 1555 1555 1.75 LINK ZN ZN A 3 O HOH A 12 1555 1555 2.29 LINK ZN ZN A 3 OE1 GLU A 97 1555 1555 2.07 LINK ZN ZN A 4 SG CYS A 44 1555 1555 2.32 LINK ZN ZN A 5 OE2 GLU A 46 1555 1555 2.27 LINK ZN ZN A 5 O HOH A 218 1555 1555 2.28 LINK ZN ZN A 5 O HOH A 225 1555 1555 2.39 SITE 1 AC1 6 ZN A 4 CYS A 44 GLU A 47 ASP A 153 SITE 2 AC1 6 HOH A 217 HOH A 226 SITE 1 AC2 4 GLU A 113 GLU A 160 HOH A 237 HOH A 238 SITE 1 AC3 4 HOH A 12 GLU A 97 ASP A 152 HOH A 173 SITE 1 AC4 6 ZN A 1 HOH A 8 CYS A 44 ASP A 153 SITE 2 AC4 6 HOH A 218 HOH A 240 SITE 1 AC5 4 GLU A 46 GLU A 145 HOH A 218 HOH A 225 SITE 1 AC6 4 GLN A 120 TYR A 123 HOH A 227 ALA M 170 CRYST1 44.021 44.021 266.840 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 0.022716 0.013115 0.000000 0.00000 SCALE2 0.000000 0.026231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003748 0.00000