PDB Short entry for 2EZD HEADER DNA BINDING PROTEIN/DNA 04-JUN-97 2EZD TITLE SOLUTION STRUCTURE OF A COMPLEX OF THE SECOND DNA BINDING DOMAIN OF TITLE 2 HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF TITLE 3 THE INTERFERON-BETA PROMOTER, NMR, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: HIGH MOBILITY GROUP PROTEIN HMG; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA BINDING PROTEIN, MINOR GROOVE DNA BINDING, TRANSCRIPTIONAL CO- KEYWDS 2 ACTIVATOR, ARCHITECTURAL FACTOR, COMPLEX (DNA-BINDING PROTEIN-DNA), KEYWDS 3 DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,J.R.HUTH,C.BEWLEY,A.M.GRONENBORN REVDAT 3 09-MAR-22 2EZD 1 REMARK REVDAT 2 24-FEB-09 2EZD 1 VERSN REVDAT 1 15-OCT-97 2EZD 0 JRNL AUTH J.R.HUTH,C.A.BEWLEY,M.S.NISSEN,J.N.EVANS,R.REEVES, JRNL AUTH 2 A.M.GRONENBORN,G.M.CLORE JRNL TITL THE SOLUTION STRUCTURE OF AN HMG-I(Y)-DNA COMPLEX DEFINES A JRNL TITL 2 NEW ARCHITECTURAL MINOR GROOVE BINDING MOTIF. JRNL REF NAT.STRUCT.BIOL. V. 4 657 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9253416 JRNL DOI 10.1038/NSB0897-657 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. REMARK 3 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) REMARK 3 MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. REMARK 3 (1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON REMARK 3 CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. REMARK 3 SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL REMARK 3 DATABASE REMARK 3 POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - REMARK 3 1080 REMARK 3 AND (1997) J. MAGN. RESON. 125, 171-177) REMARK 3 THE 3D STRUCTURE OF THE COMPLEX OF THE SECOND DNA BINDING REMARK 3 DOMAIN OF HMG-I(Y) REMARK 3 COMPLEXED TO DNA WAS SOLVED BY REMARK 3 MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR REMARK 3 (A) PROTEIN: 71 SEQUENTIAL (|I-J|=1), 4 MEDIUM REMARK 3 RANGE (1 < |I-J| >=5) AND 64 INTRARESIDUE REMARK 3 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL REMARK 3 36 TORSION ANGLE RESTRAINTS REMARK 3 13 THREE-BOND HN-HA AND 8 THREE_BOND COCO COUPLING REMARK 3 CONSTANT RESTRAINTS; 39 (21 CALPHA AND 18 CBETA) 13C REMARK 3 SHIFT RESTRAINTS. REMARK 3 (B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND REMARK 3 33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42 REMARK 3 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 136 REMARK 3 TORSION ANGLE RESTRAINTS REMARK 3 (C) 73 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS REMARK 3 (D) 5 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES REMARK 3 (E) 20 'REPULSIVE' RESTRAINTS REMARK 3 REMARK 3 THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED REMARK 3 MEAN STRUCTURE. THE LAST NUMERIC COLUMN REPRESENTS THE REMARK 3 RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES REMARK 3 FOUND IN PDB ENTRY 2EZE ABOUT THE MEAN COORDINATE REMARK 3 POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA REMARK 3 STRUCTURES HAS NO MEANING. REMARK 3 REMARK 3 RESIDUES 3 - 27 OF THE PROTEIN CORRESPOND TO RESIDUES 51 - REMARK 3 75 OF INTACT HMG-I(Y). RESIDUES 3 - 5 AND 20 - 27 ARE REMARK 3 DISORDERED. ONLY RESIDUES 3 - 23 ARE PROVIDED FOR THE REMARK 3 RESTRAINED REGULARIZED MEAN STRUCTURE. REMARK 4 REMARK 4 2EZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178055. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 306 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AMX500; AMX600; DMX600; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR MODIFIED MODIFIED REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 35 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DATA WERE RECORDED ON A 2:1 COMPLEX OF DNA DODECAMER TO REMARK 210 HMG-I(Y) 50-91 WHICH CONTAINS THE SECOND AND THIRD DNA REMARK 210 DNA BINDING DOMAINS. EACH DNA BINDING DOMAIN BINDS TO REMARK 210 1 MOLECULE OF DNA. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 THR A 24 REMARK 465 ARG A 25 REMARK 465 LYS A 26 REMARK 465 THR A 27 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 PRO A 6 81.01 -49.94 REMARK 500 PRO A 13 153.61 -42.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EZE RELATED DB: PDB REMARK 900 ENSEMBLE OF 35 STRUCTURES DBREF 2EZD A 3 23 UNP P17096 HMGIY_HUMAN 39 59 DBREF 2EZD B 201 212 PDB 2EZD 2EZD 201 212 DBREF 2EZD C 213 224 PDB 2EZD 2EZD 213 224 SEQRES 1 B 12 DG DG DG DA DA DA DT DT DC DC DT DC SEQRES 1 C 12 DG DA DG DG DA DA DT DT DT DC DC DC SEQRES 1 A 25 VAL PRO THR PRO LYS ARG PRO ARG GLY ARG PRO LYS GLY SEQRES 2 A 25 SER LYS ASN LYS GLY ALA ALA LYS THR ARG LYS THR 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