PDB Short entry for 2YRQ HEADER DNA BINDING PROTEIN 02-APR-07 2YRQ TITLE SOLUTION STRUCTURE OF THE TANDEM HMG BOX DOMAIN FROM HUMAN HIGH TITLE 2 MOBILITY GROUP PROTEIN B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN B1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HMG BOX DOMAIN; COMPND 5 SYNONYM: HIGH MOBILITY GROUP PROTEIN 1, HMG-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: HMGB1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P061030-05; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS HMG BOX DOMAIN, DNA BINDING, HELIX-TURN-HELIX MOTIF, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.TOMIZAWA,S.KOSHIBA,S.WATANABE,T.HARADA,T.KIGAWA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 16-MAR-22 2YRQ 1 REMARK SEQADV REVDAT 2 24-FEB-09 2YRQ 1 VERSN REVDAT 1 12-FEB-08 2YRQ 0 JRNL AUTH T.TOMIZAWA,S.KOSHIBA,S.WATANABE,T.HARADA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE TANDEM HMG BOX DOMAIN FROM HUMAN JRNL TITL 2 HIGH MOBILITY GROUP PROTEIN B1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (TOPSPIN), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YRQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027050. 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 : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.09MM HMG BOX DOMAIN U-15N,13C; REMARK 210 20MM D-TRIS-HCL (PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20060524, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9823, 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 : 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 3 101.61 -46.95 REMARK 500 1 SER A 6 137.54 -172.30 REMARK 500 1 PRO A 16 92.36 -69.79 REMARK 500 1 ALA A 24 -33.70 -38.00 REMARK 500 1 LYS A 35 -25.59 -39.40 REMARK 500 1 ASP A 40 31.72 -90.62 REMARK 500 1 SER A 53 -71.53 -60.83 REMARK 500 1 PRO A 88 -174.97 -69.76 REMARK 500 1 LYS A 93 44.56 39.10 REMARK 500 1 LYS A 95 31.63 35.34 REMARK 500 1 LEU A 127 178.29 -56.94 REMARK 500 1 GLU A 152 -62.25 -90.88 REMARK 500 2 SER A 5 149.42 -38.72 REMARK 500 2 MET A 8 143.85 -35.48 REMARK 500 2 LYS A 15 121.62 -34.51 REMARK 500 2 LYS A 35 -34.19 -34.73 REMARK 500 2 SER A 53 -71.31 -60.13 REMARK 500 2 MET A 59 135.03 -39.04 REMARK 500 2 GLU A 91 45.23 -80.68 REMARK 500 2 ALA A 171 106.63 -161.66 REMARK 500 3 SER A 2 163.33 -48.68 REMARK 500 3 LYS A 10 -60.55 -101.79 REMARK 500 3 ARG A 17 42.29 -98.89 REMARK 500 3 SER A 53 -72.03 -65.64 REMARK 500 3 ALA A 101 155.89 -41.28 REMARK 500 3 PRO A 106 -178.97 -69.73 REMARK 500 3 LEU A 127 -175.49 -58.08 REMARK 500 3 ILE A 129 -36.81 -35.61 REMARK 500 3 LYS A 172 47.42 -87.59 REMARK 500 4 LYS A 19 141.33 -37.10 REMARK 500 4 ALA A 24 -38.42 -33.82 REMARK 500 4 SER A 53 -71.59 -57.99 REMARK 500 4 PRO A 88 -174.60 -69.72 REMARK 500 4 LYS A 95 174.33 -46.97 REMARK 500 4 ALA A 101 141.82 -36.01 REMARK 500 4 ILE A 129 -36.29 -35.16 REMARK 500 5 LYS A 15 130.87 -34.95 REMARK 500 5 LYS A 19 135.29 -35.48 REMARK 500 5 SER A 53 -71.58 -67.35 REMARK 500 5 PRO A 88 -171.29 -69.75 REMARK 500 5 LYS A 89 102.09 -45.76 REMARK 500 5 PHE A 96 123.17 -173.01 REMARK 500 5 PRO A 106 -179.13 -69.74 REMARK 500 5 LEU A 127 -178.60 -50.69 REMARK 500 5 THR A 143 149.89 -37.80 REMARK 500 5 LYS A 172 -37.82 -34.64 REMARK 500 6 LYS A 19 126.63 -35.72 REMARK 500 6 LYS A 35 -25.96 -39.29 REMARK 500 6 SER A 42 42.95 -89.94 REMARK 500 6 PHE A 48 -31.88 -39.96 REMARK 500 REMARK 500 THIS ENTRY HAS 212 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSB001016428.1 RELATED DB: TARGETDB DBREF 2YRQ A 8 173 UNP P09429 HMGB1_HUMAN 1 166 SEQADV 2YRQ GLY A 1 UNP P09429 EXPRESSION TAG SEQADV 2YRQ SER A 2 UNP P09429 EXPRESSION TAG SEQADV 2YRQ SER A 3 UNP P09429 EXPRESSION TAG SEQADV 2YRQ GLY A 4 UNP P09429 EXPRESSION TAG SEQADV 2YRQ SER A 5 UNP P09429 EXPRESSION TAG SEQADV 2YRQ SER A 6 UNP P09429 EXPRESSION TAG SEQADV 2YRQ GLY A 7 UNP P09429 EXPRESSION TAG SEQRES 1 A 173 GLY SER SER GLY SER SER GLY MET GLY LYS GLY ASP PRO SEQRES 2 A 173 LYS LYS PRO ARG GLY LYS MET SER SER TYR ALA PHE PHE SEQRES 3 A 173 VAL GLN THR CYS ARG GLU GLU HIS LYS LYS LYS HIS PRO SEQRES 4 A 173 ASP ALA SER VAL ASN PHE SER GLU PHE SER LYS LYS CYS SEQRES 5 A 173 SER GLU ARG TRP LYS THR MET SER ALA LYS GLU LYS GLY SEQRES 6 A 173 LYS PHE GLU ASP MET ALA LYS ALA ASP LYS ALA ARG TYR SEQRES 7 A 173 GLU ARG GLU MET LYS THR TYR ILE PRO PRO LYS GLY GLU SEQRES 8 A 173 THR LYS LYS LYS PHE LYS ASP PRO ASN ALA PRO LYS ARG SEQRES 9 A 173 PRO PRO SER ALA PHE PHE LEU PHE CYS SER GLU TYR ARG SEQRES 10 A 173 PRO LYS ILE LYS GLY GLU HIS PRO GLY LEU SER ILE GLY SEQRES 11 A 173 ASP VAL ALA LYS LYS LEU GLY GLU MET TRP ASN ASN THR SEQRES 12 A 173 ALA ALA ASP ASP LYS GLN PRO TYR GLU LYS LYS ALA ALA SEQRES 13 A 173 LYS LEU LYS GLU LYS TYR GLU LYS ASP ILE ALA ALA TYR SEQRES 14 A 173 ARG ALA LYS GLY HELIX 1 1 SER A 21 HIS A 38 1 18 HELIX 2 2 ASN A 44 MET A 59 1 16 HELIX 3 3 SER A 60 TYR A 78 1 19 HELIX 4 4 TYR A 78 TYR A 85 1 8 HELIX 5 5 SER A 107 HIS A 124 1 18 HELIX 6 6 SER A 128 THR A 143 1 16 HELIX 7 7 ALA A 144 ASP A 146 5 3 HELIX 8 8 ASP A 147 ALA A 171 1 25 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