PDB Short entry for 2GZK HEADER DNA/STRUCTURAL PROTEIN 11-MAY-06 2GZK TITLE STRUCTURE OF A COMPLEX OF TANDEM HMG BOXES AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SEX-DETERMINING REGION ON Y / HMGB1; COMPND 11 CHAIN: A; COMPND 12 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, RATTUS RATTUS; SOURCE 7 ORGANISM_COMMON: HUMAN, BLACK RAT; SOURCE 8 ORGANISM_TAXID: 9606,10117; SOURCE 9 STRAIN: ,; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, HMG BOX, AMPHOTERIN, DNA-STRUCTURAL PROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR AUTHOR K.STOTT,G.S.TANG,K.B.LEE,J.O.THOMAS REVDAT 3 09-MAR-22 2GZK 1 REMARK REVDAT 2 24-FEB-09 2GZK 1 VERSN REVDAT 1 25-JUL-06 2GZK 0 JRNL AUTH K.STOTT,G.S.TANG,K.B.LEE,J.O.THOMAS JRNL TITL STRUCTURE OF A COMPLEX OF TANDEM HMG BOXES AND DNA. JRNL REF J.MOL.BIOL. V. 360 90 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16813837 JRNL DOI 10.1016/J.JMB.2006.04.059 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.7, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER, A. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037742. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 10MM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM SRY.B U-15N,13C, 1MM 16-MER REMARK 210 DNA, 10MM PHOSPHATE BUFFER, PH REMARK 210 6.8, 1MM EDTA, 2MM DTT U-2H, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC; 3D HN(CO)CA; HNCA-J; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCO; REMARK 210 3D (H)CC(CO)NH-TOCSY; 3D TOCSY- REMARK 210 15N-HSQC; 3D NOESY-15N-HSQC; 3D REMARK 210 HCCH-TOCSY; 3D NOESY-13C-HSQC; REMARK 210 HNHA; 2D TOCSY; DQF-COSY; 2D REMARK 210 NOESY; [F1]-13C/15N-FILTERED REMARK 210 TOCSY [F1]-13C/15N-FILTERED REMARK 210 TOCSY; 2D [F1]-13C/15N-FILTERED REMARK 210 DQF COSY; 2D [F1]-13C/15N- REMARK 210 FILTERED NOESY; 3D [F1]-13C/15N- REMARK 210 FILTERED NOESY-13C-HSQC; 2D [F1, REMARK 210 F2]-13C/15N-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AZARA 2.7, ANALYSIS 1.0, CNS 1.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: 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 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 HZ2 LYS A 76 OE1 GLU A 78 1.52 REMARK 500 OE2 GLU A 78 HZ2 LYS A 81 1.58 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 ASP A 3 46.94 -84.37 REMARK 500 MET A 30 50.89 34.12 REMARK 500 ASN A 71 -52.94 -130.15 REMARK 500 LYS A 76 98.74 -67.28 REMARK 500 GLU A 78 -118.11 -73.12 REMARK 500 THR A 79 -127.19 -174.34 REMARK 500 LYS A 81 37.80 -88.68 REMARK 500 PRO A 112 49.94 -77.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7105 RELATED DB: BMRB REMARK 900 NMR CHEMICAL SHIFT ASSIGNMENTS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN IS A CHIMERIC PROTEIN, A HYBRID, MADE FROM REMARK 999 THE HMG-BOX DOMAIN FROM HUMAN SRY, COMPRISING RESIDUES REMARK 999 56-130 FOLLOWED BY RESIDUES 82-165 OF RAT HMGB1 DBREF 2GZK A 1 75 UNP Q6J4I5 Q6J415_HUMAN 56 130 DBREF 2GZK A 76 159 UNP Q548R9 Q548R9_RAT 82 165 DBREF 2GZK B 201 216 PDB 2GZK 2GZK 201 216 DBREF 2GZK C 217 232 PDB 2GZK 2GZK 217 232 SEQRES 1 B 16 DG DG DG DA DT DC DT DA DA DA DC DA DA SEQRES 2 B 16 DT DG DC SEQRES 1 C 16 DG DC DA DT DT DG DT DT DT DA DG DA DT SEQRES 2 C 16 DC DC DC SEQRES 1 A 159 VAL GLN ASP ARG VAL LYS ARG PRO MET ASN ALA PHE ILE SEQRES 2 A 159 VAL TRP SER ARG ASP GLN ARG ARG LYS MET ALA LEU GLU SEQRES 3 A 159 ASN PRO ARG MET ARG ASN SER GLU ILE SER LYS GLN LEU SEQRES 4 A 159 GLY TYR GLN TRP LYS MET LEU THR GLU ALA GLU LYS TRP SEQRES 5 A 159 PRO PHE PHE GLN GLU ALA GLN LYS LEU GLN ALA MET HIS SEQRES 6 A 159 ARG GLU LYS TYR PRO ASN TYR LYS TYR ARG LYS GLY GLU SEQRES 7 A 159 THR LYS LYS LYS PHE LYS ASP PRO ASN ALA PRO LYS ARG SEQRES 8 A 159 PRO PRO SER ALA PHE PHE LEU PHE CYS SER GLU TYR ARG SEQRES 9 A 159 PRO LYS ILE LYS GLY GLU HIS PRO GLY LEU SER ILE GLY SEQRES 10 A 159 ASP VAL ALA LYS LYS LEU GLY GLU MET TRP ASN ASN THR SEQRES 11 A 159 ALA ALA ASP ASP LYS GLN PRO TYR GLU LYS LYS ALA ALA SEQRES 12 A 159 LYS LEU LYS GLU LYS TYR GLU LYS ASP ILE ALA ALA TYR SEQRES 13 A 159 ARG ALA LYS HELIX 1 1 ASN A 10 ASN A 27 1 18 HELIX 2 2 ARG A 31 LEU A 46 1 16 HELIX 3 3 THR A 47 TYR A 69 1 23 HELIX 4 4 THR A 79 PHE A 83 5 5 HELIX 5 5 SER A 94 HIS A 111 1 18 HELIX 6 6 SER A 115 THR A 130 1 16 HELIX 7 7 ALA A 131 ALA A 158 1 28 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