PDB Short entry for 1J5N HEADER DNA BINDING PROTEIN/DNA 15-MAY-02 1J5N TITLE SOLUTION STRUCTURE OF THE NON-SEQUENCE-SPECIFIC HMGB PROTEIN NHP6A IN TITLE 2 COMPLEX WITH SRY DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SRY_DNA G-RICH STRAND; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: SRY_DNA C-RICH STRAND; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NONHISTONE CHROMOSOMAL PROTEIN 6A; COMPND 13 CHAIN: A; COMPND 14 SYNONYM: NHP6A; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: UNLABELED DNA MADE ON A COMMERCIAL SYNTHESIZER, 15N, SOURCE 4 13C-LABELED DNA MADE ENZYMATICALLY IN VITRO WITH TAQ POLYMERASE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: UNLABELED DNA MADE ON A COMMERCIAL SYNTHESIZER, 15N, SOURCE 8 13C-LABELED DNA MADE ENZYMATICALLY IN VITRO WITH TAQ POLYMERASE; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HMG-BOX, HMGB, PROTEIN-DNA COMPLEX, ALPHA HELIX, DOUBLE HELIX, DNA KEYWDS 2 BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.E.MASSE,B.WONG,Y.-M.YEN,F.H.-T.ALLAIN,R.C.JOHNSON,J.FEIGON REVDAT 3 23-FEB-22 1J5N 1 REMARK REVDAT 2 24-FEB-09 1J5N 1 VERSN REVDAT 1 16-OCT-02 1J5N 0 JRNL AUTH J.E.MASSE,B.WONG,Y.-M.YEN,F.H.-T.ALLAIN,R.C.JOHNSON,J.FEIGON JRNL TITL THE S. CEREVISIAE ARCHITECTURAL HMGB PROTEIN NHP6A COMPLEXED JRNL TITL 2 WITH DNA: DNA AND PROTEIN CONFORMATIONAL CHANGES UPON JRNL TITL 3 BINDING JRNL REF J.MOL.BIOL. V. 323 263 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12381320 JRNL DOI 10.1016/S0022-2836(02)00938-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 3035 RESTRAINTS. REMARK 3 102 ARE FROM ALPHA-HELICAL HYDROGEN BOND RESTRAINTS WITHIN THE REMARK 3 PROTEIN (2/H-BOND). REMARK 3 76 ARE HYDROGEN BOND RESTRAINTS FOR WATSON-CRICK BASE PAIRS IN THE REMARK 3 DNA. THE REST REMARK 3 ARE NOE-DERIVED. 2197 OF THE NOE RESTRAINTS ARE PROTEIN-PROTEIN REMARK 3 RESTRAINTS, 578 REMARK 3 ARE DNA-DNA RESTRAINTS, AND 82 ARE PROTEIN-DNA RESTRAINTS. REMARK 4 REMARK 4 1J5N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000001642. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 283 REMARK 210 PH : 5.8; 5.8 REMARK 210 IONIC STRENGTH : 2 MM NAPO4, 10 MM NACL; 2 MM REMARK 210 NAPO4, 10 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : PROTEIN AND DNA UNLABELED, 2MM REMARK 210 SAMPLE 90% H2O, 10% D2O OR 100% REMARK 210 D2O; UNIFORM LABELING WITH 15N REMARK 210 OF PROTEIN, DNA UNLABELED, 2MM REMARK 210 90% H2O, 10% D2O; UNIFORM REMARK 210 LABELING WITH 15N,13C OF PROTEIN, REMARK 210 DNA UNLABELED, 2MM 100% D2O; REMARK 210 UNIFORM LABELING WITH 15N,13C OF REMARK 210 DNA (BOTH STRANDS), PROTEIN REMARK 210 UNLABELED, 2MM 100% D2O; UNIFORM REMARK 210 LABELING WITH 15N,13C OF G-RICH REMARK 210 DNA STRAND AND PROTEIN, C-RICH REMARK 210 DNA STRAND UNLABELED, 2MM 100% REMARK 210 D2O; UNIFORM LABELING WITH 15N, REMARK 210 13C OF C-RICH DNA STRAND AND REMARK 210 PROTEIN, G-RICH DNA STRAND REMARK 210 UNLABELED, 2MM 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_13C-FILTERED_NOESY_TMIX=50; REMARK 210 2D_13C-FILTERED_NOESY_TMIX=100; 2D_13C-FILTERED_NOESY_TMIX=150; REMARK 210 2D_13C-FILTERED_NOESY_TMIX=200; 2D_13C-FILTERED_NOESY_TMIX=250; REMARK 210 2D_13C-FILTERED_NOESY_TMIX=300; 3D_15N-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_13C_DOUBLE-HALF-FILTERED_13C-SEPARATED_NOESY; REMARK 210 2D_11_ECHO_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE CALCULATED USING STANDARD 3D HETERONUCLEAR REMARK 210 FILTERING AND EDITING TECHNIQUES WITH BOTH LABELED PROTEIN AND REMARK 210 LABELED 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DG B 101 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 101 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 102 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG B 102 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 103 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 103 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 104 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG B 104 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 105 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 105 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 106 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 107 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA B 107 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT B 108 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 108 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT B 108 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 109 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 109 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT B 109 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 110 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG B 110 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT B 111 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 111 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT B 112 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 112 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC B 113 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 113 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA B 114 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 114 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG B 115 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG B 115 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC C 116 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT C 117 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT C 117 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT C 117 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG C 118 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG C 118 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA C 119 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA C 120 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA C 120 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC C 121 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC C 121 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA C 122 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA C 122 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA C 123 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA C 123 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT C 124 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT C 124 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DC C 125 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC C 125 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1147 ANGLE DEVIATIONS. 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 LYS A 8 49.35 -151.30 REMARK 500 1 LYS A 9 92.40 40.72 REMARK 500 1 THR A 11 120.11 161.12 REMARK 500 1 THR A 12 48.35 36.34 REMARK 500 1 ARG A 13 151.26 -36.14 REMARK 500 1 LYS A 14 -166.16 -61.13 REMARK 500 1 LYS A 16 82.56 168.12 REMARK 500 1 ASP A 17 150.28 157.35 REMARK 500 1 ALA A 20 78.99 50.52 REMARK 500 1 LYS A 22 54.51 88.60 REMARK 500 1 ARG A 23 -151.79 29.84 REMARK 500 1 LEU A 25 -169.64 -58.13 REMARK 500 1 ASN A 35 -73.66 -66.90 REMARK 500 1 ARG A 36 -63.75 -10.07 REMARK 500 1 GLN A 50 -53.37 -127.02 REMARK 500 1 LEU A 62 -71.47 -52.80 REMARK 500 1 THR A 63 147.16 136.07 REMARK 500 1 THR A 91 -41.63 -141.75 REMARK 500 2 PRO A 7 -175.53 -51.58 REMARK 500 2 LYS A 8 -34.40 -177.49 REMARK 500 2 LYS A 9 -39.01 -160.00 REMARK 500 2 THR A 11 -83.09 -33.28 REMARK 500 2 THR A 12 81.12 53.00 REMARK 500 2 ARG A 13 115.94 -33.29 REMARK 500 2 LYS A 15 143.90 -37.90 REMARK 500 2 LYS A 16 126.37 -175.99 REMARK 500 2 ASP A 17 149.39 85.63 REMARK 500 2 ALA A 20 103.54 45.26 REMARK 500 2 LYS A 22 79.68 95.37 REMARK 500 2 ARG A 23 151.23 -25.01 REMARK 500 2 ALA A 24 170.05 -58.07 REMARK 500 2 LEU A 25 -167.18 -69.97 REMARK 500 2 ASN A 35 -70.09 -63.67 REMARK 500 2 ARG A 36 -63.64 -9.74 REMARK 500 2 ILE A 38 -71.06 -58.61 REMARK 500 2 ASP A 45 33.76 -99.37 REMARK 500 2 THR A 47 147.46 100.11 REMARK 500 2 PHE A 48 -85.48 -36.54 REMARK 500 2 LEU A 62 -78.00 -58.31 REMARK 500 2 THR A 63 148.70 150.96 REMARK 500 2 GLU A 82 -34.26 -38.98 REMARK 500 2 TYR A 88 -39.91 -37.11 REMARK 500 2 THR A 91 -46.55 -133.89 REMARK 500 3 VAL A 2 92.80 36.35 REMARK 500 3 PRO A 4 94.17 -69.70 REMARK 500 3 PRO A 7 174.58 -52.01 REMARK 500 3 LYS A 9 91.82 -173.23 REMARK 500 3 ARG A 10 -157.12 36.55 REMARK 500 3 THR A 11 -61.97 161.25 REMARK 500 3 ARG A 13 141.50 -33.27 REMARK 500 REMARK 500 THIS ENTRY HAS 420 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CG7 RELATED DB: PDB REMARK 900 FREE NHP6A PROTEIN STRUCTURE DBREF 1J5N A 1 93 UNP P11632 NHP6A_YEAST 1 93 DBREF 1J5N B 101 115 PDB 1J5N 1J5N 101 115 DBREF 1J5N C 116 130 PDB 1J5N 1J5N 116 130 SEQRES 1 B 15 DG DG DG DG DT DG DA DT DT DG DT DT DC SEQRES 2 B 15 DA DG SEQRES 1 C 15 DC DT DG DA DA DC DA DA DT DC DA DC DC SEQRES 2 C 15 DC DC SEQRES 1 A 93 MET VAL THR PRO ARG GLU PRO LYS LYS ARG THR THR ARG SEQRES 2 A 93 LYS LYS LYS ASP PRO ASN ALA PRO LYS ARG ALA LEU SER SEQRES 3 A 93 ALA TYR MET PHE PHE ALA ASN GLU ASN ARG ASP ILE VAL SEQRES 4 A 93 ARG SER GLU ASN PRO ASP ILE THR PHE GLY GLN VAL GLY SEQRES 5 A 93 LYS LYS LEU GLY GLU LYS TRP LYS ALA LEU THR PRO GLU SEQRES 6 A 93 GLU LYS GLN PRO TYR GLU ALA LYS ALA GLN ALA ASP LYS SEQRES 7 A 93 LYS ARG TYR GLU SER GLU LYS GLU LEU TYR ASN ALA THR SEQRES 8 A 93 LEU ALA HELIX 1 1 SER A 26 ASN A 43 1 18 HELIX 2 2 THR A 47 THR A 63 1 17 HELIX 3 3 THR A 63 ALA A 93 1 31 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