HEADER DNA BINDING PROTEIN 30-MAR-07 2YQE
TITLE SOLUTION STRUCTURE OF THE ARID DOMAIN OF JARID1D PROTEIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1D;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ARID DOMAIN;
COMPND 5 SYNONYM: PROTEIN SMCY, HISTOCOMPATIBILITY Y ANTIGEN, H-Y;
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: SMCY, HY, HYA, JARID1D, KIAA0234;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060731-15
KEYWDS ARID DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN
KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL
KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR W.TANABE,S.SUZUKI,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU,
AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 4 29-MAY-24 2YQE 1 REMARK
REVDAT 3 16-MAR-22 2YQE 1 REMARK SEQADV
REVDAT 2 24-FEB-09 2YQE 1 VERSN
REVDAT 1 01-APR-08 2YQE 0
JRNL AUTH W.TANABE,S.SUZUKI,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,
JRNL AUTH 2 M.SHIROUZU,S.YOKOYAMA
JRNL TITL SOLUTION STRUCTURE OF THE ARID DOMAIN OF JARID1D PROTEIN
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 2.1
REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2YQE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-07.
REMARK 100 THE DEPOSITION ID IS D_1000027002.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 120MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 20MM D-TRIS-HCL(PH7.0); 100MM
REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90%
REMARK 210 H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 20060702, NMRVIEW 5.0.4,
REMARK 210 KUJIRA 0.9820, CYANA 2.1
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY, TARGET
REMARK 210 FUNCTION
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 76 135.40 -170.53
REMARK 500 1 THR A 79 38.58 -94.84
REMARK 500 1 ARG A 80 -74.14 -79.29
REMARK 500 1 LYS A 82 -27.87 -39.86
REMARK 500 1 GLU A 94 -31.96 -39.31
REMARK 500 1 ARG A 107 41.68 36.94
REMARK 500 1 ARG A 132 41.28 35.36
REMARK 500 1 TRP A 134 -37.44 -38.28
REMARK 500 1 ASN A 148 72.93 -66.53
REMARK 500 1 HIS A 156 -39.22 -36.96
REMARK 500 1 GLN A 168 41.27 -84.69
REMARK 500 2 THR A 79 95.87 -49.42
REMARK 500 2 TYR A 85 -32.89 -39.53
REMARK 500 2 GLU A 94 -36.91 -39.17
REMARK 500 2 ARG A 132 50.87 39.07
REMARK 500 2 LYS A 147 179.99 -59.85
REMARK 500 2 ASN A 148 42.22 -93.97
REMARK 500 3 ARG A 80 -63.42 -124.87
REMARK 500 3 LYS A 82 -31.92 -35.13
REMARK 500 3 SER A 99 173.26 -55.51
REMARK 500 3 ALA A 127 -70.46 -65.58
REMARK 500 3 ARG A 132 37.99 36.04
REMARK 500 3 PRO A 145 96.68 -69.77
REMARK 500 3 ASN A 148 75.99 -62.87
REMARK 500 3 TYR A 157 -70.27 -68.57
REMARK 500 4 GLN A 88 -71.03 -72.26
REMARK 500 4 SER A 98 110.27 -167.02
REMARK 500 4 SER A 99 163.28 -43.84
REMARK 500 4 ARG A 132 44.56 36.98
REMARK 500 4 ASN A 148 81.39 -66.68
REMARK 500 4 SER A 169 96.09 -60.12
REMARK 500 5 SER A 99 166.68 -49.88
REMARK 500 5 ARG A 132 35.92 34.39
REMARK 500 5 HIS A 142 35.82 71.91
REMARK 500 5 SER A 155 -71.93 -61.34
REMARK 500 5 HIS A 156 -34.94 -37.37
REMARK 500 5 GLN A 168 38.07 -96.03
REMARK 500 6 ARG A 80 -53.69 -123.94
REMARK 500 6 LYS A 82 -30.33 -36.93
REMARK 500 6 ARG A 132 52.23 34.31
REMARK 500 6 PRO A 145 94.80 -69.79
REMARK 500 6 LYS A 147 168.55 -49.56
REMARK 500 6 ASN A 148 43.80 -83.39
REMARK 500 6 GLN A 168 49.52 -75.65
REMARK 500 7 SER A 76 91.69 -56.71
REMARK 500 7 LYS A 82 -31.10 -35.90
REMARK 500 7 ARG A 132 43.43 34.46
REMARK 500 7 HIS A 142 48.88 71.42
REMARK 500 7 PRO A 145 95.27 -69.80
REMARK 500 7 ASN A 148 81.14 -63.76
REMARK 500
REMARK 500 THIS ENTRY HAS 142 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: HSO002001234.3 RELATED DB: TARGETDB
DBREF 2YQE A 79 171 UNP Q9BY66 JAD1D_HUMAN 79 171
SEQADV 2YQE GLY A 72 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE SER A 73 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE SER A 74 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE GLY A 75 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE SER A 76 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE SER A 77 UNP Q9BY66 EXPRESSION TAG
SEQADV 2YQE GLY A 78 UNP Q9BY66 EXPRESSION TAG
SEQRES 1 A 100 GLY SER SER GLY SER SER GLY THR ARG VAL LYS LEU ASN
SEQRES 2 A 100 TYR LEU ASP GLN ILE ALA LYS PHE TRP GLU ILE GLN GLY
SEQRES 3 A 100 SER SER LEU LYS ILE PRO ASN VAL GLU ARG LYS ILE LEU
SEQRES 4 A 100 ASP LEU TYR SER LEU SER LYS ILE VAL ILE GLU GLU GLY
SEQRES 5 A 100 GLY TYR GLU ALA ILE CYS LYS ASP ARG ARG TRP ALA ARG
SEQRES 6 A 100 VAL ALA GLN ARG LEU HIS TYR PRO PRO GLY LYS ASN ILE
SEQRES 7 A 100 GLY SER LEU LEU ARG SER HIS TYR GLU ARG ILE ILE TYR
SEQRES 8 A 100 PRO TYR GLU MET PHE GLN SER GLY ALA
HELIX 1 1 ARG A 80 GLY A 97 1 18
HELIX 2 2 ASP A 111 GLY A 123 1 13
HELIX 3 3 GLY A 124 ASP A 131 1 8
HELIX 4 4 ARG A 133 LEU A 141 1 9
HELIX 5 5 ASN A 148 ILE A 160 1 13
HELIX 6 6 ILE A 160 GLN A 168 1 9
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
