HEADER DNA BINDING PROTEIN 21-OCT-99 1D8B TITLE NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ TITLE 2 HELICASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SGS1 RECQ HELICASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HRDC DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: MODIFIED PET9D KEYWDS FIVE HELICES, THREE-HELICAL BUNDLE FLANKED BY TWO HELICES, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Z.LIU,M.J.MACIAS,M.J.BOTTOMLEY,G.STIER,J.P.LINGE,M.NILGES,P.BORK, AUTHOR 2 M.SATTLER REVDAT 4 22-MAY-24 1D8B 1 REMARK REVDAT 3 16-FEB-22 1D8B 1 REMARK REVDAT 2 24-FEB-09 1D8B 1 VERSN REVDAT 1 10-JAN-00 1D8B 0 JRNL AUTH Z.LIU,M.J.MACIAS,M.J.BOTTOMLEY,G.STIER,J.P.LINGE,M.NILGES, JRNL AUTH 2 P.BORK,M.SATTLER JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE HRDC DOMAIN AND JRNL TITL 2 IMPLICATIONS FOR THE WERNER AND BLOOM SYNDROME PROTEINS. JRNL REF STRUCTURE FOLD.DES. V. 7 1557 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10647186 JRNL DOI 10.1016/S0969-2126(00)88346-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.7, CNS 0.9 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER, ADAMS, CLORE, DELANO, REMARK 3 GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, REMARK 3 PANNU, READ, RICE, SIMONSON, WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STARTING WITH AN ALMOST COMPLETE LIST REMARK 3 OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN REMARK 3 ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED REMARK 3 AMBIGUOUS DISTANCE RESTRAINTS FROM DIFFERENT NOE SPECTRA AND REMARK 3 ASSIGNS THE NOE PEAKS IN AN ITERATIVE MANNER. FROM A TOTAL OF REMARK 3 1890 NOES ABOUT 85% WERE MANUALLY ASSIGNED, THE REMAINDER WAS REMARK 3 ASSIGNED BY ARIA. FLOATING POINT CHIRALITY ASSIGNMENT WAS USED REMARK 3 DURING THE STRUCTURE CALCULATION IN ORDER TO OBTAIN REMARK 3 STEREOSPECIFIC ASSIGNMENTS FOR METHYL AND METHYLENE GROUPS. REMARK 3 THEREFORE, SOME METHYL AND METHYLENE CARBON/PROTON ATOM NAMES IN REMARK 3 THE RESTRAINT FILES MIGHT BE INCONSISTENT COMPARED TO THOSE IN REMARK 3 THE COORIDINATE FILES. THE DEPOSITED STRUCTURES HAVE BEEN WATER- REMARK 3 REFINED AS DESCRIBED IN THE PUBLICATION. PSI REFINEMENT: THE REMARK 3 STRUCTURES HAVE BEEN DIRECTLY REFINED AGAINST CROSS- CORRELATED REMARK 3 RELAXATION RATES (C-ALPHA-H-ALPHA DIPOLE, CO CSA) AND THE THREE- REMARK 3 BOND H/D ISOTOPE EFFECT ON THE C-ALPHA CHEMICAL SHIFT. " REMARK 3 REFINEMENT OF THE PROTEIN BACKBONE ANGLE PSI IN NMR STRUCTURE REMARK 3 CALCULATIONS." SPRANGERS, BOTTOMLEY, LINGE, SCHULTZ, NILGES, REMARK 3 SATTLER. REMARK 4 REMARK 4 1D8B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009879. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 13C-15N-LABELED SAMPLE; 15N REMARK 210 -LABELED SAMPLE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, ARIA 0.9, CNS 0.9 REMARK 210 METHOD USED : ARIA (AMBIGUOUS RESTRAINTS IN REMARK 210 ITERATIVE ASSIGNMENTS) AMBIGUOUS REMARK 210 DISTANCE RESTRAINTS SIMULATED REMARK 210 ANNEALING WITH TORSION ANGLE REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON- BOND 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 O LEU A 22 HG SER A 26 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 14 PHE A 40 CE1 PHE A 40 CZ 0.125 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 ASN A 13 101.46 -56.49 REMARK 500 2 LEU A 53 72.38 50.61 REMARK 500 2 MET A 55 30.70 -99.86 REMARK 500 2 THR A 65 78.49 49.35 REMARK 500 2 SER A 89 -56.90 68.74 REMARK 500 2 SER A 90 -56.41 -145.42 REMARK 500 3 LEU A 12 42.92 -91.20 REMARK 500 3 ASN A 13 37.30 -86.51 REMARK 500 3 ASN A 39 75.20 -111.87 REMARK 500 3 PHE A 40 -72.49 -22.38 REMARK 500 3 LEU A 53 72.09 52.89 REMARK 500 3 SER A 90 -132.27 -118.38 REMARK 500 4 PHE A 40 -86.55 -57.78 REMARK 500 4 THR A 65 75.58 -153.72 REMARK 500 4 SER A 89 -46.30 -133.73 REMARK 500 5 ASN A 39 60.34 -102.87 REMARK 500 5 PHE A 40 -79.96 -38.50 REMARK 500 5 THR A 65 111.92 -164.89 REMARK 500 5 SER A 89 -12.46 78.65 REMARK 500 6 LEU A 53 75.40 54.94 REMARK 500 6 THR A 65 69.54 -101.55 REMARK 500 6 ARG A 88 46.82 -80.79 REMARK 500 7 LEU A 12 48.85 -91.94 REMARK 500 7 ASP A 57 -176.34 -68.07 REMARK 500 7 SER A 58 -49.28 70.45 REMARK 500 7 ARG A 88 49.35 -82.54 REMARK 500 8 ASN A 13 47.67 -92.55 REMARK 500 8 ASN A 39 73.08 -102.49 REMARK 500 8 PHE A 40 -75.47 -43.69 REMARK 500 8 THR A 65 82.11 56.67 REMARK 500 8 SER A 90 39.95 -143.72 REMARK 500 9 LEU A 53 73.70 59.38 REMARK 500 9 ARG A 72 -76.65 -56.68 REMARK 500 9 SER A 90 -46.05 72.25 REMARK 500 10 ASN A 13 37.08 -88.49 REMARK 500 10 ASN A 39 64.50 -119.85 REMARK 500 10 LEU A 53 71.52 54.46 REMARK 500 10 SER A 90 -75.72 -146.70 REMARK 500 11 ASN A 13 37.73 -88.35 REMARK 500 11 LEU A 53 70.83 50.57 REMARK 500 11 THR A 65 79.65 51.09 REMARK 500 12 ASN A 13 91.64 -57.70 REMARK 500 12 VAL A 34 100.88 59.76 REMARK 500 12 PHE A 40 -78.79 -50.38 REMARK 500 12 GLU A 67 150.76 -49.44 REMARK 500 13 ASN A 39 66.19 -105.87 REMARK 500 13 LEU A 53 75.75 59.02 REMARK 500 13 THR A 65 77.78 48.56 REMARK 500 14 ASN A 13 34.99 -94.90 REMARK 500 14 PHE A 40 -77.36 -48.48 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D8B A 11 91 UNP P35187 SGS1_YEAST 1271 1351 SEQRES 1 A 81 GLU LEU ASN ASN LEU ARG MET THR TYR GLU ARG LEU ARG SEQRES 2 A 81 GLU LEU SER LEU ASN LEU GLY ASN ARG MET VAL PRO PRO SEQRES 3 A 81 VAL GLY ASN PHE MET PRO ASP SER ILE LEU LYS LYS MET SEQRES 4 A 81 ALA ALA ILE LEU PRO MET ASN ASP SER ALA PHE ALA THR SEQRES 5 A 81 LEU GLY THR VAL GLU ASP LYS TYR ARG ARG ARG PHE LYS SEQRES 6 A 81 TYR PHE LYS ALA THR ILE ALA ASP LEU SER LYS LYS ARG SEQRES 7 A 81 SER SER GLU HELIX 1 1 ASN A 13 MET A 33 1 21 HELIX 2 2 ASP A 43 ALA A 51 1 9 HELIX 3 3 ALA A 59 THR A 62 5 4 HELIX 4 4 ASP A 68 PHE A 74 1 7 HELIX 5 5 PHE A 77 ARG A 88 1 12 CISPEP 1 VAL A 34 PRO A 35 1 0.03 CISPEP 2 VAL A 34 PRO A 35 2 0.20 CISPEP 3 VAL A 34 PRO A 35 3 -0.12 CISPEP 4 VAL A 34 PRO A 35 4 0.94 CISPEP 5 VAL A 34 PRO A 35 5 -0.22 CISPEP 6 VAL A 34 PRO A 35 6 0.32 CISPEP 7 VAL A 34 PRO A 35 7 0.06 CISPEP 8 VAL A 34 PRO A 35 8 -0.29 CISPEP 9 VAL A 34 PRO A 35 9 0.09 CISPEP 10 VAL A 34 PRO A 35 10 0.55 CISPEP 11 VAL A 34 PRO A 35 11 0.42 CISPEP 12 VAL A 34 PRO A 35 12 0.17 CISPEP 13 VAL A 34 PRO A 35 13 0.50 CISPEP 14 VAL A 34 PRO A 35 14 0.27 CISPEP 15 VAL A 34 PRO A 35 15 -0.01 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