HEADER GENE REGULATION 31-MAR-06 2DJB
TITLE SOLUTION STRUCTURE OF THE RING DOMAIN OF THE HUMAN POLYCOMB GROUP RING
TITLE 2 FINGER PROTEIN 6
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: POLYCOMB GROUP RING FINGER PROTEIN 6;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RING DOMAIN;
COMPND 5 SYNONYM: RING FINGER PROTEIN 134, MEL18 AND BMI1-LIKE RING FINGER;
COMPND 6 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: PCGF6, MBLR, RNF134;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050302-15;
SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS POLYCOMB GROUP RING FINGER PROTEIN 6, RING FINGER PROTEIN 134, PCGF6,
KEYWDS 2 RING DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON
KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL
KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, GENE REGULATION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR K.MIYAMOTO,T.KIGAWA,M.SATO,S.KOSHIBA,M.INOUE,S.YOKOYAMA,RIKEN
AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 09-MAR-22 2DJB 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 2DJB 1 VERSN
REVDAT 1 13-MAR-07 2DJB 0
JRNL AUTH K.MIYAMOTO,T.KIGAWA,M.SATO,S.KOSHIBA,M.INOUE,S.YOKOYAMA
JRNL TITL SOLUTION STRUCTURE OF THE RING DOMAIN OF THE HUMAN POLYCOMB
JRNL TITL 2 GROUP RING FINGER PROTEIN 6
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17
REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2DJB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-06.
REMARK 100 THE DEPOSITION ID IS D_1000025480.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 296
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 120
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.43MM RING DOMAIN U-13C,15N;
REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM
REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3;
REMARK 210 0.05MM ZNCL2; 1.0MM IDA; 90% H2O,
REMARK 210 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4,
REMARK 210 KUJIRA 0.9732, CYANA 2.0.17
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH
REMARK 210 THE LEAST RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 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 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 1 SER A 2 -61.71 -92.17
REMARK 500 1 PRO A 14 3.36 -69.83
REMARK 500 1 ILE A 16 -35.91 -38.87
REMARK 500 1 ILE A 20 -65.82 -99.43
REMARK 500 1 ILE A 26 -61.99 -120.35
REMARK 500 1 ALA A 28 47.61 74.74
REMARK 500 1 GLU A 33 -68.99 -109.30
REMARK 500 1 ASN A 51 33.81 -81.84
REMARK 500 1 PRO A 54 10.00 -69.77
REMARK 500 1 ASN A 57 46.78 73.96
REMARK 500 1 HIS A 61 56.82 -97.36
REMARK 500 1 GLN A 62 -61.33 -105.43
REMARK 500 1 PRO A 69 -169.20 -69.77
REMARK 500 1 SER A 70 40.94 -94.72
REMARK 500 2 LEU A 12 53.56 -116.33
REMARK 500 2 ILE A 16 -36.98 -36.36
REMARK 500 2 LYS A 22 36.98 37.80
REMARK 500 2 LEU A 25 86.83 -65.51
REMARK 500 2 ALA A 28 137.73 -31.32
REMARK 500 2 THR A 32 -39.08 -31.01
REMARK 500 2 ASN A 51 43.68 -78.95
REMARK 500 2 PRO A 54 8.39 -69.78
REMARK 500 2 ASN A 57 54.45 71.39
REMARK 500 2 VAL A 59 79.23 -69.91
REMARK 500 2 PRO A 65 84.24 -69.81
REMARK 500 2 LEU A 66 99.65 -56.64
REMARK 500 2 SER A 71 42.29 -84.97
REMARK 500 3 ILE A 16 71.84 -66.50
REMARK 500 3 ALA A 28 54.89 70.63
REMARK 500 3 THR A 32 -35.45 -32.82
REMARK 500 3 LEU A 35 47.60 38.27
REMARK 500 3 ILE A 43 -32.92 -38.73
REMARK 500 3 ASN A 51 49.22 -75.33
REMARK 500 3 PRO A 54 9.39 -69.80
REMARK 500 3 LYS A 55 -65.79 -121.96
REMARK 500 3 VAL A 59 88.80 -62.99
REMARK 500 3 GLN A 62 -56.61 -120.94
REMARK 500 3 THR A 63 -56.81 -124.29
REMARK 500 3 LEU A 66 144.47 -34.83
REMARK 500 3 PRO A 69 -179.02 -69.78
REMARK 500 4 SER A 3 -60.18 -122.13
REMARK 500 4 SER A 5 43.63 38.40
REMARK 500 4 PRO A 14 -179.05 -69.76
REMARK 500 4 TYR A 15 40.20 -87.33
REMARK 500 4 ASP A 27 52.99 -114.97
REMARK 500 4 ALA A 28 135.68 -27.29
REMARK 500 4 THR A 32 -35.93 -32.09
REMARK 500 4 PRO A 54 6.56 -69.73
REMARK 500 4 LYS A 55 -69.98 -108.52
REMARK 500 4 ASN A 57 51.48 74.97
REMARK 500
REMARK 500 THIS ENTRY HAS 232 RAMACHANDRAN OUTLIERS.
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 201 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 18 SG
REMARK 620 2 CYS A 21 SG 119.2
REMARK 620 3 CYS A 39 SG 107.3 105.1
REMARK 620 4 CYS A 42 SG 119.1 87.0 117.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 401 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 34 SG
REMARK 620 2 HIS A 36 ND1 87.3
REMARK 620 3 CYS A 53 SG 106.5 120.6
REMARK 620 4 CYS A 56 SG 93.9 120.9 115.4
REMARK 620 N 1 2 3
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED
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 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
DBREF 2DJB A 8 66 UNP Q9BYE7 PCGF6_HUMAN 126 184
SEQADV 2DJB GLY A 1 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 2 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 3 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB GLY A 4 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 5 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 6 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB GLY A 7 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 67 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB GLY A 68 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB PRO A 69 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 70 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB SER A 71 UNP Q9BYE7 CLONING ARTIFACT
SEQADV 2DJB GLY A 72 UNP Q9BYE7 CLONING ARTIFACT
SEQRES 1 A 72 GLY SER SER GLY SER SER GLY ASN LEU SER GLU LEU THR
SEQRES 2 A 72 PRO TYR ILE LEU CYS SER ILE CYS LYS GLY TYR LEU ILE
SEQRES 3 A 72 ASP ALA THR THR ILE THR GLU CYS LEU HIS THR PHE CYS
SEQRES 4 A 72 LYS SER CYS ILE VAL ARG HIS PHE TYR TYR SER ASN ARG
SEQRES 5 A 72 CYS PRO LYS CYS ASN ILE VAL VAL HIS GLN THR GLN PRO
SEQRES 6 A 72 LEU SER GLY PRO SER SER GLY
HET ZN A 201 1
HET ZN A 401 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 CYS A 39 SER A 50 1 12
SHEET 1 A 2 THR A 29 THR A 30 0
SHEET 2 A 2 THR A 37 PHE A 38 -1 O PHE A 38 N THR A 29
LINK SG CYS A 18 ZN ZN A 201 1555 1555 2.32
LINK SG CYS A 21 ZN ZN A 201 1555 1555 2.32
LINK SG CYS A 34 ZN ZN A 401 1555 1555 2.33
LINK ND1 HIS A 36 ZN ZN A 401 1555 1555 2.30
LINK SG CYS A 39 ZN ZN A 201 1555 1555 2.35
LINK SG CYS A 42 ZN ZN A 201 1555 1555 2.33
LINK SG CYS A 53 ZN ZN A 401 1555 1555 2.32
LINK SG CYS A 56 ZN ZN A 401 1555 1555 2.31
SITE 1 AC1 4 CYS A 18 CYS A 21 CYS A 39 CYS A 42
SITE 1 AC2 5 CYS A 34 HIS A 36 CYS A 53 LYS A 55
SITE 2 AC2 5 CYS A 56
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
