HEADER GENE REGULATION, APOPTOSIS 24-FEB-06 2G6Q
TITLE CRYSTAL STRUCTURE OF ING2 PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INHIBITOR OF GROWTH PROTEIN 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PHD DOMAIN (RESIDUES 204-263);
COMPND 5 SYNONYM: P33ING2, INHIBITOR OF GROWTH 1-LIKE PROTEIN, ING1LP, P32;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: H3K4ME3 PEPTIDE;
COMPND 9 CHAIN: B;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 GENE: ING2, ING1L;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 OTHER_DETAILS: H3K4ME3 IS CHEMICALLY SYNTHESIZED
KEYWDS PROTEIN-PEPTIDE COMPLEX, PHD FINGER, GENE REGULATION, APOPTOSIS
EXPDTA X-RAY DIFFRACTION
AUTHOR P.V.PENA,R.ZHAO,T.G.KUTATELADZE
REVDAT 4 30-AUG-23 2G6Q 1 REMARK SEQADV LINK
REVDAT 3 24-JUL-13 2G6Q 1 KEYWDS TITLE VERSN
REVDAT 2 24-FEB-09 2G6Q 1 VERSN
REVDAT 1 11-JUL-06 2G6Q 0
JRNL AUTH P.V.PENA,F.DAVRAZOU,X.SHI,K.L.WALTER,V.V.VERKHUSHA,O.GOZANI,
JRNL AUTH 2 R.ZHAO,T.G.KUTATELADZE
JRNL TITL MOLECULAR MECHANISM OF HISTONE H3K4ME3 RECOGNITION BY PLANT
JRNL TITL 2 HOMEODOMAIN OF ING2.
JRNL REF NATURE V. 442 100 2006
JRNL REFN ISSN 0028-0836
JRNL PMID 16728977
JRNL DOI 10.1038/NATURE04814
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 5074
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.223
REMARK 3 FREE R VALUE : 0.231
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 527
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2345
REMARK 3 BIN FREE R VALUE : 0.2388
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 488
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 2
REMARK 3 SOLVENT ATOMS : 32
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 28.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.080
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2G6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-06.
REMARK 100 THE DEPOSITION ID IS D_1000036757.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-FEB-06
REMARK 200 TEMPERATURE (KELVIN) : 93
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5116
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
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 (%) : 97.0
REMARK 200 DATA REDUNDANCY : 4.400
REMARK 200 R MERGE (I) : 0.03900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 51.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07
REMARK 200 COMPLETENESS FOR SHELL (%) : 79.6
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : 0.09400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 18.50
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: PDB ENTRY 1WES
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 22% PEGMME2K, 0.01M
REMARK 280 NICL2(6H2O), PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
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 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 35.09667
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 17.54833
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.54833
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 35.09667
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 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 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 203
REMARK 465 SER A 204
REMARK 465 GLU A 205
REMARK 465 PHE A 206
REMARK 465 ALA A 207
REMARK 465 ILE A 208
REMARK 465 ASP A 209
REMARK 465 PRO A 210
REMARK 465 ASN A 211
REMARK 465 GLU A 264
REMARK 465 LYS B 9
REMARK 465 SER B 10
REMARK 465 THR B 11
REMARK 465 GLY B 12
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 216 -172.38 63.33
REMARK 500 GLU A 237 -64.47 76.74
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 300 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 216 SG
REMARK 620 2 CYS A 218 SG 116.4
REMARK 620 3 HIS A 240 ND1 100.2 98.8
REMARK 620 4 CYS A 243 SG 103.6 118.7 118.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 400 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 229 SG
REMARK 620 2 CYS A 234 SG 111.6
REMARK 620 3 CYS A 256 SG 113.3 110.8
REMARK 620 4 CYS A 259 SG 105.5 111.8 103.4
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 300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1WES RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF ING1 PHD DOMAIN
DBREF 2G6Q A 205 264 UNP Q9ESK4 ING2_MOUSE 205 264
DBREF 2G6Q B 1 12 PDB 2G6Q 2G6Q 1 12
SEQADV 2G6Q GLY A 203 UNP Q9ESK4 CLONING ARTIFACT
SEQADV 2G6Q SER A 204 UNP Q9ESK4 CLONING ARTIFACT
SEQRES 1 A 62 GLY SER GLU PHE ALA ILE ASP PRO ASN GLU PRO THR TYR
SEQRES 2 A 62 CYS LEU CYS ASN GLN VAL SER TYR GLY GLU MET ILE GLY
SEQRES 3 A 62 CYS ASP ASN GLU GLN CYS PRO ILE GLU TRP PHE HIS PHE
SEQRES 4 A 62 SER CYS VAL SER LEU THR TYR LYS PRO LYS GLY LYS TRP
SEQRES 5 A 62 TYR CYS PRO LYS CYS ARG GLY ASP ASN GLU
SEQRES 1 B 12 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY
MODRES 2G6Q M3L B 4 LYS N-TRIMETHYLLYSINE
HET M3L B 4 12
HET ZN A 300 1
HET ZN A 400 1
HETNAM M3L N-TRIMETHYLLYSINE
HETNAM ZN ZINC ION
FORMUL 2 M3L C9 H21 N2 O2 1+
FORMUL 3 ZN 2(ZN 2+)
FORMUL 5 HOH *32(H2 O)
HELIX 1 1 SER A 242 SER A 245 5 4
HELIX 2 2 CYS A 256 GLY A 261 1 6
SHEET 1 A 2 THR A 214 TYR A 215 0
SHEET 2 A 2 GLN A 220 VAL A 221 -1 O GLN A 220 N TYR A 215
SHEET 1 B 3 TRP A 238 HIS A 240 0
SHEET 2 B 3 GLU A 225 GLY A 228 -1 N ILE A 227 O PHE A 239
SHEET 3 B 3 ARG B 2 GLN B 5 -1 O ARG B 2 N GLY A 228
LINK C THR B 3 N M3L B 4 1555 1555 1.33
LINK C M3L B 4 N GLN B 5 1555 1555 1.32
LINK SG CYS A 216 ZN ZN A 300 1555 1555 2.48
LINK SG CYS A 218 ZN ZN A 300 1555 1555 2.41
LINK SG CYS A 229 ZN ZN A 400 1555 1555 2.34
LINK SG CYS A 234 ZN ZN A 400 1555 1555 2.39
LINK ND1 HIS A 240 ZN ZN A 300 1555 1555 2.24
LINK SG CYS A 243 ZN ZN A 300 1555 1555 2.33
LINK SG CYS A 256 ZN ZN A 400 1555 1555 2.37
LINK SG CYS A 259 ZN ZN A 400 1555 1555 2.42
SITE 1 AC1 4 CYS A 216 CYS A 218 HIS A 240 CYS A 243
SITE 1 AC2 4 CYS A 229 CYS A 234 CYS A 256 CYS A 259
CRYST1 49.176 49.176 52.645 90.00 90.00 120.00 P 32 2 1 6
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 0.020335 0.011740 0.000000 0.00000
SCALE2 0.000000 0.023481 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018995 0.00000
(ATOM LINES ARE NOT SHOWN.)
END