PDB Short entry for 1LWM HEADER DNA BINDING PROTEIN 31-MAY-02 1LWM TITLE SOLUTION STRUCTURE OF THE SEQUENCE-NON-SPECIFIC HMGB PROTEIN NHP6A COMPND MOL_ID: 1; COMPND 2 MOLECULE: NONHISTONE CHROMOSOMAL PROTEIN 6A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NHP6A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: NHP6A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HMG-BOX, HMGB, ALPHA HELIX, DNA BINDING PROTEIN 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 1LWM 1 REMARK REVDAT 2 24-FEB-09 1LWM 1 VERSN REVDAT 1 16-OCT-02 1LWM 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: THE STRUCTURES ARE BASED ON THE SAME REMARK 3 RESTRAINTS AS PREVIOUSLY USED IN THE 1999 STRUCTURE 1CG7, BUT REMARK 3 DIFFERENT A-HELIX HYDROGEN BOND RESTRAINTS WERE INCLUDED. THESE REMARK 3 ARE THE SAME AS THOSE USED TO CALCULATE THE STRUCTURE OF THE REMARK 3 COMPLEX WITH SRY_DNA. REMARK 4 REMARK 4 1LWM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016351. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 10 MM NAPO4, 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 2MM 15N-LABELED NHP6A; 2MM REMARK 210 13C/15N-LABELED NHP6A REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_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 : XWINNMR 2.6, FELIX 2000, X-PLOR REMARK 210 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE CALCULATED USING THE SAME DATA AS REMARK 210 PREVIOUSLY USED IN THE 1999 STRUCTURE 1CG7 BUT USING NEW A-HELIX REMARK 210 HYDROGEN BOND RESTRAINTS AND XPLOR INSTEAD OF DYANA. 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 THR A 3 93.97 58.17 REMARK 500 1 PRO A 7 97.02 -51.80 REMARK 500 1 LYS A 8 63.88 36.95 REMARK 500 1 ARG A 10 105.14 57.70 REMARK 500 1 THR A 11 67.61 -118.17 REMARK 500 1 PRO A 18 -174.86 -69.41 REMARK 500 1 ASN A 19 81.16 36.95 REMARK 500 1 ARG A 23 107.92 64.33 REMARK 500 1 ASN A 43 77.37 -162.19 REMARK 500 1 THR A 63 139.10 -35.13 REMARK 500 2 VAL A 2 -88.87 58.24 REMARK 500 2 ARG A 5 98.99 48.44 REMARK 500 2 GLU A 6 108.71 52.61 REMARK 500 2 ARG A 10 29.59 -143.40 REMARK 500 2 THR A 12 -162.76 -105.01 REMARK 500 2 LYS A 14 -77.32 -174.96 REMARK 500 2 ASP A 17 80.41 50.18 REMARK 500 2 PRO A 18 -160.47 -52.55 REMARK 500 2 ASN A 19 103.08 -50.32 REMARK 500 2 LYS A 22 -81.18 -100.71 REMARK 500 2 ARG A 23 110.06 -174.99 REMARK 500 2 ALA A 24 171.78 -43.66 REMARK 500 3 LYS A 8 -90.03 62.20 REMARK 500 3 THR A 12 98.49 -66.73 REMARK 500 3 ARG A 13 41.80 -99.27 REMARK 500 3 LYS A 14 -46.23 84.63 REMARK 500 3 LYS A 15 145.44 63.82 REMARK 500 3 PRO A 18 -164.24 -51.88 REMARK 500 3 ASN A 19 94.44 52.44 REMARK 500 3 ALA A 20 86.90 -177.59 REMARK 500 3 ALA A 24 -153.57 45.95 REMARK 500 3 ASN A 43 71.94 -151.29 REMARK 500 3 THR A 47 -167.72 -119.36 REMARK 500 3 THR A 63 139.68 -35.40 REMARK 500 4 VAL A 2 56.02 -108.22 REMARK 500 4 GLU A 6 152.71 177.78 REMARK 500 4 LYS A 8 33.19 70.07 REMARK 500 4 LYS A 9 132.13 170.70 REMARK 500 4 ARG A 10 99.82 -36.53 REMARK 500 4 ASP A 17 55.38 -159.30 REMARK 500 4 PRO A 18 -175.50 -69.84 REMARK 500 4 ASN A 19 79.43 43.24 REMARK 500 4 ALA A 20 58.31 -152.21 REMARK 500 4 LYS A 22 -71.22 -65.77 REMARK 500 4 ARG A 23 135.77 178.31 REMARK 500 4 ALA A 24 174.76 -45.80 REMARK 500 4 ASN A 43 75.55 -158.63 REMARK 500 4 THR A 63 114.99 -35.08 REMARK 500 5 VAL A 2 54.53 -112.62 REMARK 500 5 ARG A 5 76.79 40.97 REMARK 500 REMARK 500 THIS ENTRY HAS 221 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 (1999) REMARK 900 RELATED ID: 1J5N RELATED DB: PDB REMARK 900 NHP6A/SRY_DNA COMPLEX REMARK 900 RELATED ID: 1LWA RELATED DB: PDB REMARK 900 FREE SRY_DNA STRUCTURE DBREF 1LWM A 1 93 UNP P11632 NHP6A_YEAST 1 93 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 ALA A 61 1 15 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