HEADER CELL CYCLE 04-FEB-08 2VNF TITLE MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY ING4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INHIBITOR OF GROWTH PROTEIN 4; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: RESIDUES 187-245; COMPND 5 SYNONYM: ING 4, P29ING4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H3; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: RESIDUES 2-11; SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11D; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS ACETYLATION, ALTERNATIVE SPLICING, ANTI-ONCOGENE, CELL KEYWDS 2 CYCLE, COILED C NUCLEUS, ZINC, ZINC-FINGER, ING4, PHD KEYWDS 3 FINGER, HISTONE 3 EXPDTA X-RAY DIFFRACTION AUTHOR A.PALACIOS,I.G.MUNOZ,D.PANTOJA-UCEDA,M.J.MARCAIDA,D.TORRES, AUTHOR 2 J.M.MARTIN-GARCIA,I.LUQUE,G.MONTOYA,F.J.BLANCO REVDAT 5 28-DEC-16 2VNF 1 COMPND SOURCE REMARK VERSN REVDAT 5 2 DBREF SEQADV FORMUL REVDAT 4 04-AUG-09 2VNF 1 SOURCE REMARK SEQRES MODRES REVDAT 4 2 HET LINK SITE HETATM REVDAT 4 3 ANISOU ATOM TER CONECT REVDAT 4 4 MASTER REVDAT 3 24-FEB-09 2VNF 1 VERSN REVDAT 2 17-JUN-08 2VNF 1 JRNL REVDAT 1 01-APR-08 2VNF 0 JRNL AUTH A.PALACIOS,I.G.MUNOZ,D.PANTOJA-UCEDA,M.J.MARCAIDA, JRNL AUTH 2 D.TORRES,J.M.MARTIN-GARCIA,I.LUQUE,G.MONTOYA, JRNL AUTH 3 F.J.BLANCO JRNL TITL MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY JRNL TITL 2 ING4 JRNL REF J.BIOL.CHEM. V. 283 15956 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18381289 JRNL DOI 10.1074/JBC.M710020200 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 12178 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 635 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 757 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 1.09000 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): 0.198 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.340 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 994 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1345 ; 1.816 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 118 ;12.226 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ;33.318 ;23.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 145 ;19.534 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.705 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 140 ; 0.179 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 752 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 546 ; 0.328 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 687 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 100 ; 0.511 ; 0.200 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): 42 ; 0.391 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.829 ; 0.200 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): 601 ; 3.343 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 966 ; 4.771 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 417 ; 7.057 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 379 ; 9.192 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2VNF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-08. REMARK 100 THE PDBE ID CODE IS EBI-34935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.76 REMARK 200 RESOLUTION RANGE LOW (A) : 68.51 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.8 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.6 REMARK 200 R MERGE FOR SHELL (I) : 0.38 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.70 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: PDB ENTRY 2G6Q REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.08700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.13050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 7.04350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1220 ANGSTROM**2 REMARK 350 TOTAL SURFACE AREA FOR THE COMPLEX: 4490 ANGSTROM**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 TOTAL SURFACE AREA FOR THE COMPLEX: 5330 ANGSTROM**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 187 REMARK 465 ASP A 188 REMARK 465 MET A 189 REMARK 465 PRO A 190 REMARK 465 VAL A 191 REMARK 465 ASP A 192 REMARK 465 PRO A 193 REMARK 465 ASN A 194 REMARK 465 GLU A 245 REMARK 465 ARG A 246 REMARK 465 ALA B 7 REMARK 465 ARG B 8 REMARK 465 LYS B 9 REMARK 465 SER B 10 REMARK 465 MET C 187 REMARK 465 ASP C 188 REMARK 465 MET C 189 REMARK 465 PRO C 190 REMARK 465 GLU C 245 REMARK 465 ARG C 246 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 ARG A 234 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 240 CB CG CD REMARK 470 VAL C 191 CG1 CG2 REMARK 470 ARG C 234 CG CD NE CZ NH1 NH2 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 CE1 HIS A 202 - C1 DTT A 1245 1.85 REMARK 500 NE2 HIS A 202 - C4 DTT A 1245 1.99 REMARK 500 N PRO A 240 - O HOH A 2054 1.57 REMARK 500 OE1 GLN A 244 - O HOH A 2060 2.10 REMARK 500 CE1 HIS C 202 - S4 DTU C 1246 2.11 REMARK 500 NE2 HIS C 202 - O2 DTU C 1246 1.85 REMARK 500 O HOH D 2015 - O HOH D 2017 2.12 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 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 199 173.29 75.89 REMARK 500 GLU A 220 -46.61 78.22 REMARK 500 ASP C 192 81.92 96.05 REMARK 500 CYS C 199 175.12 76.80 REMARK 500 GLU C 220 -55.27 73.52 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 SER A 243 GLN A 244 -143.34 REMARK 500 VAL C 191 ASP C 192 136.40 REMARK 500 LYS D 9 SER D 10 -119.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--N1(N9)--O4'--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG D 8 16.6 L L OUTSIDE RANGE REMARK 500 SER D 10 25.0 L L OUTSIDE RANGE 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 NA A 300 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2059 O REMARK 620 2 HOH A2061 O 64.1 REMARK 620 3 HOH A2058 O 146.8 129.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1248 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 212 SG REMARK 620 2 CYS C 242 SG 109.6 REMARK 620 3 CYS C 217 SG 111.5 109.4 REMARK 620 4 CYS C 239 SG 116.2 101.1 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1246 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 201 SG REMARK 620 2 HIS A 223 ND1 94.6 REMARK 620 3 CYS A 199 SG 116.2 101.8 REMARK 620 4 CYS A 226 SG 117.0 118.7 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1247 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 212 SG REMARK 620 2 CYS A 217 SG 110.1 REMARK 620 3 CYS A 239 SG 115.8 112.5 REMARK 620 4 CYS A 242 SG 108.8 106.1 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1247 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 199 SG REMARK 620 2 CYS C 201 SG 116.5 REMARK 620 3 HIS C 223 ND1 102.6 95.3 REMARK 620 4 CYS C 226 SG 109.3 115.4 116.6 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 NA A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A1245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTU C1246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1247 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ING4(RESIDUES 188-246) DBREF 2VNF A 188 246 UNP Q9UNL4 ING4_HUMAN 188 246 DBREF 2VNF B 1 10 UNP Q5TEC6 Q5TEC6_HUMAN 2 11 DBREF 2VNF C 188 246 UNP Q9UNL4 ING4_HUMAN 188 246 DBREF 2VNF D 1 10 UNP Q5TEC6 Q5TEC6_HUMAN 2 11 SEQADV 2VNF MET A 187 UNP Q9UNL4 EXPRESSION TAG SEQADV 2VNF MET C 187 UNP Q9UNL4 EXPRESSION TAG SEQRES 1 A 60 MET ASP MET PRO VAL ASP PRO ASN GLU PRO THR TYR CYS SEQRES 2 A 60 LEU CYS HIS GLN VAL SER TYR GLY GLU MET ILE GLY CYS SEQRES 3 A 60 ASP ASN PRO ASP CYS SER ILE GLU TRP PHE HIS PHE ALA SEQRES 4 A 60 CYS VAL GLY LEU THR THR LYS PRO ARG GLY LYS TRP PHE SEQRES 5 A 60 CYS PRO ARG CYS SER GLN GLU ARG SEQRES 1 B 10 ALA ARG THR M3L GLN THR ALA ARG LYS SER SEQRES 1 C 60 MET ASP MET PRO VAL ASP PRO ASN GLU PRO THR TYR CYS SEQRES 2 C 60 LEU CYS HIS GLN VAL SER TYR GLY GLU MET ILE GLY CYS SEQRES 3 C 60 ASP ASN PRO ASP CYS SER ILE GLU TRP PHE HIS PHE ALA SEQRES 4 C 60 CYS VAL GLY LEU THR THR LYS PRO ARG GLY LYS TRP PHE SEQRES 5 C 60 CYS PRO ARG CYS SER GLN GLU ARG SEQRES 1 D 10 ALA ARG THR M3L GLN THR ALA ARG LYS SER MODRES 2VNF M3L B 4 LYS N-TRIMETHYLLYSINE MODRES 2VNF M3L D 4 LYS N-TRIMETHYLLYSINE HET M3L B 4 12 HET M3L D 4 12 HET NA A 300 1 HET DTT A1245 8 HET DTU C1246 8 HET ZN A1246 1 HET ZN C1247 1 HET ZN C1248 1 HET ZN A1247 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM NA SODIUM ION HETNAM ZN ZINC ION HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM DTU (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL FORMUL 5 M3L 2(C9 H21 N2 O2 1+) FORMUL 6 NA NA 1+ FORMUL 7 ZN 4(ZN 2+) FORMUL 8 DTT C4 H10 O2 S2 FORMUL 9 DTU C4 H10 O2 S2 FORMUL 10 HOH *127(H2 O) HELIX 1 1 ALA A 225 GLY A 228 5 4 HELIX 2 2 CYS A 239 GLN A 244 1 6 HELIX 3 3 ALA C 225 GLY C 228 5 4 SHEET 1 AA 2 THR A 197 TYR A 198 0 SHEET 2 AA 2 GLN A 203 VAL A 204 -1 O GLN A 203 N TYR A 198 SHEET 1 AB 2 MET A 209 GLY A 211 0 SHEET 2 AB 2 TRP A 221 HIS A 223 -1 O PHE A 222 N ILE A 210 SHEET 1 CA 2 THR C 197 TYR C 198 0 SHEET 2 CA 2 GLN C 203 VAL C 204 -1 O GLN C 203 N TYR C 198 SHEET 1 CB 2 MET C 209 GLY C 211 0 SHEET 2 CB 2 TRP C 221 HIS C 223 -1 O PHE C 222 N ILE C 210 LINK NA NA A 300 O HOH A2059 1555 3554 2.28 LINK NA NA A 300 O HOH A2061 1555 1555 2.58 LINK NA NA A 300 O HOH A2058 1555 3554 2.10 LINK ZN ZN A1246 SG CYS A 201 1555 1555 2.37 LINK ZN ZN A1246 ND1 HIS A 223 1555 1555 2.11 LINK ZN ZN A1246 SG CYS A 199 1555 1555 2.33 LINK ZN ZN A1246 SG CYS A 226 1555 1555 2.30 LINK ZN ZN A1247 SG CYS A 217 1555 1555 2.36 LINK ZN ZN A1247 SG CYS A 212 1555 1555 2.32 LINK ZN ZN A1247 SG CYS A 242 1555 1555 2.32 LINK ZN ZN A1247 SG CYS A 239 1555 1555 2.30 LINK C THR B 3 N M3L B 4 1555 1555 1.33 LINK C M3L B 4 N GLN B 5 1555 1555 1.33 LINK ZN ZN C1247 SG CYS C 226 1555 1555 2.34 LINK ZN ZN C1247 ND1 HIS C 223 1555 1555 2.23 LINK ZN ZN C1247 SG CYS C 199 1555 1555 2.33 LINK ZN ZN C1247 SG CYS C 201 1555 1555 2.28 LINK ZN ZN C1248 SG CYS C 239 1555 1555 2.29 LINK ZN ZN C1248 SG CYS C 217 1555 1555 2.31 LINK ZN ZN C1248 SG CYS C 242 1555 1555 2.33 LINK ZN ZN C1248 SG CYS C 212 1555 1555 2.34 LINK C THR D 3 N M3L D 4 1555 1555 1.33 LINK C M3L D 4 N GLN D 5 1555 1555 1.33 SITE 1 AC1 5 GLN A 244 DTT A1245 HOH A2058 HOH A2059 SITE 2 AC1 5 HOH A2061 SITE 1 AC2 10 CYS A 199 HIS A 202 ILE A 219 NA A 300 SITE 2 AC2 10 HOH A2007 HOH A2025 HOH A2048 HOH A2057 SITE 3 AC2 10 HOH A2060 HOH A2061 SITE 1 AC3 8 HIS C 202 ASN C 214 GLN C 244 HOH C2031 SITE 2 AC3 8 HOH C2036 HOH C2039 HOH C2040 HOH C2041 SITE 1 AC4 4 CYS A 199 CYS A 201 HIS A 223 CYS A 226 SITE 1 AC5 4 CYS C 199 CYS C 201 HIS C 223 CYS C 226 SITE 1 AC6 4 CYS C 212 CYS C 217 CYS C 239 CYS C 242 SITE 1 AC7 4 CYS A 212 CYS A 217 CYS A 239 CYS A 242 CRYST1 68.516 68.516 28.174 90.00 90.00 90.00 P 43 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 0.014595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035494 0.00000