PDB Short entry for 2D7L HEADER GENE REGULATION, DNA BINDING PROTEIN 24-NOV-05 2D7L TITLE SOLUTION STRUCTURE OF THE HMG BOX DOMAIN FROM HUMAN WD REPEAT AND HMG- TITLE 2 BOX DNA BINDING PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD REPEAT AND HMG-BOX DNA BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HMG BOX DOMAIN; COMPND 5 SYNONYM: ACIDIC NUCLEOPLASMIC DNA- BINDING PROTEIN 1, AND-1; 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: WDHD1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050111-08; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS HIGH MOBILITY GROUP BOX DOMAIN, HELIX-TURN-HELIX, DNA BINDING, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, GENE REGULATION, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.TOMIZAWA,T.KIGAWA,K.SAITO,S.KOSHIBA,M.INOUE,Y.O.KAMATARI, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D7L 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D7L 1 VERSN REVDAT 1 24-MAY-06 2D7L 0 JRNL AUTH T.TOMIZAWA,T.KIGAWA,K.SAITO,S.KOSHIBA,M.INOUE,Y.O.KAMATARI, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE HMG BOX DOMAIN FROM HUMAN WD JRNL TITL 2 REPEAT AND HMG-BOX DNA BINDING PROTEIN 1 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 2D7L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025086. 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 : 1.13MM HMG BOX DOMAIN U-15N, REMARK 210 13C; 20MM D-TRIS-HCL(PH 7.0); REMARK 210 100MM NACL; 1MM D-DTT; 0.02% REMARK 210 NAN3; 90% 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 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR 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 LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 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 PRO A 9 -174.40 -69.78 REMARK 500 1 ARG A 74 40.06 35.35 REMARK 500 1 SER A 80 107.41 -47.12 REMARK 500 2 SER A 6 138.53 -34.51 REMARK 500 2 LYS A 10 140.03 -34.38 REMARK 500 2 LEU A 48 159.00 -44.75 REMARK 500 2 LYS A 72 125.49 -173.23 REMARK 500 4 LYS A 10 171.84 -59.66 REMARK 500 4 LYS A 73 47.32 37.23 REMARK 500 5 THR A 50 -30.80 -39.68 REMARK 500 5 GLU A 70 -55.32 -126.31 REMARK 500 6 PRO A 9 -179.11 -69.74 REMARK 500 6 LEU A 48 162.02 -44.60 REMARK 500 6 THR A 50 -33.58 -34.29 REMARK 500 6 ALA A 65 117.99 -39.74 REMARK 500 6 ARG A 74 133.34 -171.61 REMARK 500 6 SER A 79 148.02 -39.07 REMARK 500 7 ASP A 30 -32.84 -38.98 REMARK 500 7 LEU A 48 163.46 -43.25 REMARK 500 7 THR A 50 -30.63 -35.83 REMARK 500 7 PRO A 78 96.87 -69.75 REMARK 500 8 SER A 2 175.49 -54.88 REMARK 500 8 LEU A 48 156.55 -46.96 REMARK 500 8 THR A 50 -28.00 -37.58 REMARK 500 8 GLU A 63 105.86 -38.30 REMARK 500 8 SER A 76 158.39 -38.85 REMARK 500 9 LEU A 48 161.27 -43.35 REMARK 500 9 THR A 50 -30.93 -35.81 REMARK 500 9 THR A 64 122.66 -38.34 REMARK 500 9 ALA A 65 98.49 -47.50 REMARK 500 9 SER A 66 92.14 -49.88 REMARK 500 10 LEU A 48 159.31 -42.31 REMARK 500 10 THR A 50 -31.37 -36.00 REMARK 500 10 GLU A 63 153.92 -42.77 REMARK 500 10 THR A 64 114.85 -34.31 REMARK 500 10 SER A 66 151.76 -41.82 REMARK 500 10 SER A 76 172.48 -47.10 REMARK 500 11 PRO A 9 -177.68 -69.69 REMARK 500 11 LEU A 48 161.84 -43.21 REMARK 500 11 THR A 50 -30.62 -36.48 REMARK 500 11 GLU A 63 93.20 -47.81 REMARK 500 11 ALA A 71 143.71 -174.87 REMARK 500 11 LYS A 72 100.64 -46.15 REMARK 500 11 LYS A 73 167.94 -46.99 REMARK 500 11 SER A 80 172.62 -53.33 REMARK 500 12 LEU A 48 156.39 -43.42 REMARK 500 12 THR A 50 -32.89 -34.42 REMARK 500 12 GLU A 63 58.52 -95.54 REMARK 500 12 SER A 76 153.48 -36.61 REMARK 500 13 LYS A 10 139.71 -39.50 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002001226.1 RELATED DB: TARGETDB DBREF 2D7L A 8 75 UNP O75717 WDHD1_HUMAN 1017 1084 SEQADV 2D7L GLY A 1 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 2 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 3 UNP O75717 CLONING ARTIFACT SEQADV 2D7L GLY A 4 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 5 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 6 UNP O75717 CLONING ARTIFACT SEQADV 2D7L GLY A 7 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 76 UNP O75717 CLONING ARTIFACT SEQADV 2D7L GLY A 77 UNP O75717 CLONING ARTIFACT SEQADV 2D7L PRO A 78 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 79 UNP O75717 CLONING ARTIFACT SEQADV 2D7L SER A 80 UNP O75717 CLONING ARTIFACT SEQADV 2D7L GLY A 81 UNP O75717 CLONING ARTIFACT SEQRES 1 A 81 GLY SER SER GLY SER SER GLY ARG PRO LYS THR GLY PHE SEQRES 2 A 81 GLN MET TRP LEU GLU GLU ASN ARG SER ASN ILE LEU SER SEQRES 3 A 81 ASP ASN PRO ASP PHE SER ASP GLU ALA ASP ILE ILE LYS SEQRES 4 A 81 GLU GLY MET ILE ARG PHE ARG VAL LEU SER THR GLU GLU SEQRES 5 A 81 ARG LYS VAL TRP ALA ASN LYS ALA LYS GLY GLU THR ALA SEQRES 6 A 81 SER GLU GLY THR GLU ALA LYS LYS ARG LYS SER GLY PRO SEQRES 7 A 81 SER SER GLY HELIX 1 1 THR A 11 ASN A 28 1 18 HELIX 2 2 ASP A 33 ARG A 46 1 14 HELIX 3 3 SER A 49 ALA A 60 1 12 HELIX 4 4 ALA A 71 LYS A 75 5 5 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