HEADER DNA BINDING PROTEIN 12-SEP-13 2RTU
TITLE SOLUTION STRUCTURE OF OXIDIZED HUMAN HMGB1 A BOX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HIGH MOBILITY GROUP PROTEIN B1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: HMG BOX 1, UNP RESIDUES 1-84;
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, HMG1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A
KEYWDS DISULFIDE BOND, HIGH MOBILITY GROUP BOX 1, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR W.JING,N.TOCHIO,S.TATE
REVDAT 4 14-JUN-23 2RTU 1 SEQADV
REVDAT 3 16-OCT-19 2RTU 1 JRNL REMARK
REVDAT 2 05-JUN-19 2RTU 1 JRNL REMARK
REVDAT 1 05-MAR-14 2RTU 0
JRNL AUTH J.WANG,N.TOCHIO,A.TAKEUCHI,J.UEWAKI,N.KOBAYASHI,S.TATE
JRNL TITL REDOX-SENSITIVE STRUCTURAL CHANGE IN THE A-DOMAIN OF HMGB1
JRNL TITL 2 AND ITS IMPLICATION FOR THE BINDING TO CISPLATIN MODIFIED
JRNL TITL 3 DNA.
JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 441 701 2013
JRNL REFN ESSN 1090-2104
JRNL PMID 24427810
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : TOPSPIN, CYANA, X-PLOR NIH
REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND
REMARK 3 WUTHRICH (CYANA), SCHWIETERS, KUSZEWSKI, TJANDRA
REMARK 3 AND CLORE (X-PLOR NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2RTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-13.
REMARK 100 THE DEPOSITION ID IS D_1000150259.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 6.4
REMARK 210 IONIC STRENGTH : 200
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.5-0.6 MM [U-13C; U-15N]
REMARK 210 PROTEIN-1, 50 MM POTASSIUM
REMARK 210 PHOSPHATE-2, 10 % [U-2H] D2O-3,
REMARK 210 150 MM POTASSIUM CHLORIDE-4, 90%
REMARK 210 H2O/10% D2O; 0.5-0.6 MM [U-13C;
REMARK 210 U-15N] PROTEIN-5, 5 % C12E5/N-
REMARK 210 HEXANOL-6, 10 % U-2H D2O-7, 150
REMARK 210 MM POTASSIUM CHLORIDE-8, 50 MM
REMARK 210 POTASSIUM PHOSPHATE-9, 90% H2O/
REMARK 210 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N
REMARK 210 NOESY; 2D 1H-15N IPAP-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE, MAGRO, NMRVIEW, CYANA,
REMARK 210 SPARKY, X-PLOR NIH
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
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 THR A 25 -71.49 -77.93
REMARK 500 1 CYS A 26 -36.62 -36.72
REMARK 500 1 ASN A 40 127.91 -32.32
REMARK 500 2 GLU A 28 -77.71 -51.99
REMARK 500 2 ASN A 40 -174.35 -58.75
REMARK 500 3 LYS A 15 -106.60 -93.53
REMARK 500 3 ALA A 37 -45.91 -25.71
REMARK 500 3 LYS A 85 57.06 -91.72
REMARK 500 4 SER A 38 140.78 93.87
REMARK 500 5 THR A 25 -63.51 -90.05
REMARK 500 5 ALA A 37 -51.25 -29.81
REMARK 500 5 VAL A 39 -162.34 -125.93
REMARK 500 5 SER A 56 -177.27 -67.38
REMARK 500 6 LYS A 15 -158.27 -98.52
REMARK 500 6 VAL A 39 -136.13 -112.02
REMARK 500 7 ASN A 40 179.36 -52.34
REMARK 500 8 MET A 4 -13.62 72.85
REMARK 500 8 LYS A 6 -68.21 68.65
REMARK 500 8 LYS A 15 -168.74 -72.49
REMARK 500 8 ALA A 37 -60.97 -14.73
REMARK 500 8 SER A 38 41.26 39.89
REMARK 500 9 ARG A 13 -58.62 -152.82
REMARK 500 9 GLU A 28 -70.53 -56.51
REMARK 500 9 ASN A 40 161.61 -37.99
REMARK 500 10 MET A 4 -66.37 69.44
REMARK 500 10 ALA A 37 -75.88 -66.68
REMARK 500 10 SER A 38 150.32 73.73
REMARK 500 10 ASN A 40 131.45 -32.97
REMARK 500 11 ARG A 13 30.73 -88.81
REMARK 500 11 LYS A 15 -157.73 -101.73
REMARK 500 11 GLU A 59 -71.00 -70.56
REMARK 500 12 LYS A 10 -3.30 73.98
REMARK 500 12 LYS A 15 -165.66 -177.24
REMARK 500 12 SER A 17 -166.41 -75.21
REMARK 500 12 CYS A 26 -36.13 -35.56
REMARK 500 12 SER A 38 150.34 76.21
REMARK 500 12 ASN A 40 133.69 -37.09
REMARK 500 13 SER A 38 65.56 37.35
REMARK 500 14 ALA A 37 -94.38 59.42
REMARK 500 14 VAL A 39 -165.48 -122.08
REMARK 500 15 LYS A 15 -149.39 -85.38
REMARK 500 15 SER A 38 -55.86 54.79
REMARK 500 15 ASN A 40 141.45 -39.34
REMARK 500 15 PRO A 84 105.70 -58.16
REMARK 500 16 CYS A 26 -38.64 -34.15
REMARK 500 16 VAL A 39 104.57 -53.28
REMARK 500 16 ASN A 40 135.89 -31.88
REMARK 500 16 LYS A 85 34.90 -88.10
REMARK 500 17 CYS A 26 -17.18 -46.68
REMARK 500 17 SER A 38 146.31 90.91
REMARK 500
REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 11532 RELATED DB: BMRB
DBREF 2RTU A 4 87 UNP P09429 HMGB1_HUMAN 1 84
SEQADV 2RTU GLY A 1 UNP P09429 EXPRESSION TAG
SEQADV 2RTU SER A 2 UNP P09429 EXPRESSION TAG
SEQADV 2RTU HIS A 3 UNP P09429 EXPRESSION TAG
SEQRES 1 A 87 GLY SER HIS MET GLY LYS GLY ASP PRO LYS LYS PRO ARG
SEQRES 2 A 87 GLY LYS MET SER SER TYR ALA PHE PHE VAL GLN THR CYS
SEQRES 3 A 87 ARG GLU GLU HIS LYS LYS LYS HIS PRO ASP ALA SER VAL
SEQRES 4 A 87 ASN PHE SER GLU PHE SER LYS LYS CYS SER GLU ARG TRP
SEQRES 5 A 87 LYS THR MET SER ALA LYS GLU LYS GLY LYS PHE GLU ASP
SEQRES 6 A 87 MET ALA LYS ALA ASP LYS ALA ARG TYR GLU ARG GLU MET
SEQRES 7 A 87 LYS THR TYR ILE PRO PRO LYS GLY GLU
HELIX 1 1 SER A 17 HIS A 34 1 18
HELIX 2 2 ASN A 40 LYS A 53 1 14
HELIX 3 3 SER A 56 ASP A 70 1 15
HELIX 4 4 ASP A 70 LYS A 79 1 10
SSBOND 1 CYS A 26 CYS A 48 1555 1555 2.03
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
