Header list of 1d8b.pdb file
Complete list - b 16 2 Bytes
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 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
Complete list - b 16 2 Bytes