Header list of 1h95.pdb file
Complete list - r 25 2 Bytes
HEADER TRANSLATION FACTOR 23-FEB-01 1H95
TITLE SOLUTION STRUCTURE OF THE SINGLE-STRANDED DNA-BINDING COLD
TITLE 2 SHOCK DOMAIN (CSD) OF HUMAN Y-BOX PROTEIN 1 (YB1)
TITLE 3 DETERMINED BY NMR (10 LOWEST ENERGY STRUCTURES)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: Y-BOX BINDING PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: COLD SHOCK DOMAIN;
COMPND 5 SYNONYM: CSD;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: SINGLE STRANDED DNA BINDING COLD SHOCK
COMPND 8 DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1)
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A
KEYWDS TRANSLATION FACTOR, TRANSCRIPTION FACTOR, OB-FOLD, 5-
KEYWDS 2 STRANDED ANTI-PARALLEL BETA-BARREL, SINGLE STRANDED DNA
KEYWDS 3 BINDING, COLD SHOCK, Y-BOX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR C.P.A.M.KLOKS,C.A.E.M.SPRONK,A.HOFFMANN,G.W.VUISTER,
AUTHOR 2 S.GRZESIEK,C.W.HILBERS
REVDAT 2 24-FEB-09 1H95 1 VERSN
REVDAT 1 21-FEB-02 1H95 0
JRNL AUTH C.P.A.M.KLOKS,C.A.E.M.SPRONK,E.LASONDER,A.HOFFMANN,
JRNL AUTH 2 G.W.VUISTER,S.GRZESIEK,C.W.HILBERS
JRNL TITL THE SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES
JRNL TITL 2 OF THE COLD-SHOCK DOMAIN OF THE HUMAN Y-BOX
JRNL TITL 3 PROTEIN YB-1.
JRNL REF J.MOL.BIOL. V. 316 317 2002
JRNL REFN ISSN 0022-2836
JRNL PMID 11851341
JRNL DOI 10.1006/JMBI.2001.5334
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : MICHEAL NILGES X-PLOR X-PLOR
REMARK 3 AUTHORS : NILGES
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MD
REMARK 4
REMARK 4 1H95 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-01.
REMARK 100 THE PDBE ID CODE IS EBI-5936.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 6.7
REMARK 210 IONIC STRENGTH : 0
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-EDITED NOESY,
REMARK 210 15N-EDITED ROESY,
REMARK 210 13C-EDITED NOESY, HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 500; 600; 750
REMARK 210 SPECTROMETER MODEL : INOVA500; INOVA750;
REMARK 210 DRX600
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE, PIPP, X-PLOR
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210 FOLLOWED BY RESTRAINED MD
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE
REMARK 210 NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK
REMARK 210 DOMAIN OF HUMAN YB-1
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 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 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 3 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 3 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 7 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 7 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 8 ARG A 27 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 8 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 8 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 9 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 10 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
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 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 3 -98.61 -116.64
REMARK 500 1 ILE A 5 -61.49 -91.37
REMARK 500 1 TRP A 15 63.67 37.11
REMARK 500 1 LYS A 43 -118.54 56.75
REMARK 500 1 ARG A 47 60.07 -112.19
REMARK 500 1 TYR A 49 144.38 70.77
REMARK 500 1 LEU A 50 -81.30 -93.29
REMARK 500 1 GLU A 67 -71.23 -100.35
REMARK 500 1 GLU A 71 -162.86 -122.37
REMARK 500 2 ILE A 5 -72.87 -95.61
REMARK 500 2 LYS A 14 -87.29 -100.32
REMARK 500 2 LYS A 42 -172.53 65.34
REMARK 500 2 ASN A 44 -86.98 53.21
REMARK 500 2 LYS A 48 -157.44 66.74
REMARK 500 2 GLU A 67 -136.61 -95.37
REMARK 500 2 GLU A 71 -166.71 -107.01
REMARK 500 3 LYS A 2 -76.52 -90.58
REMARK 500 3 VAL A 4 86.76 70.73
REMARK 500 3 ILE A 5 -72.08 -80.74
REMARK 500 3 LYS A 8 75.67 59.18
REMARK 500 3 ASN A 17 76.90 -102.52
REMARK 500 3 ASN A 28 84.95 -62.48
REMARK 500 3 ASP A 29 -76.12 -159.42
REMARK 500 3 LYS A 31 81.76 55.65
REMARK 500 3 LYS A 48 -156.52 59.32
REMARK 500 3 LEU A 50 -143.21 -88.32
REMARK 500 3 GLU A 67 -145.37 -78.30
REMARK 500 3 GLU A 71 -168.10 -121.09
REMARK 500 3 ASN A 74 63.36 34.51
REMARK 500 4 LYS A 8 83.01 53.38
REMARK 500 4 THR A 30 33.89 -143.22
REMARK 500 4 TYR A 49 -147.64 -86.81
REMARK 500 4 ARG A 51 -83.21 -139.71
REMARK 500 4 GLU A 67 -89.57 -107.82
REMARK 500 5 LYS A 3 -98.90 75.38
REMARK 500 5 ASP A 29 -81.33 -76.25
REMARK 500 5 LYS A 31 62.29 77.57
REMARK 500 5 ASN A 44 -80.39 -76.73
REMARK 500 5 TYR A 49 159.74 66.32
REMARK 500 5 GLU A 67 -69.78 -101.75
REMARK 500 6 LYS A 8 73.15 60.95
REMARK 500 6 LYS A 14 -86.95 -105.37
REMARK 500 6 ASN A 28 48.00 -82.54
REMARK 500 6 THR A 30 35.33 -150.34
REMARK 500 6 LYS A 31 75.99 57.87
REMARK 500 6 LYS A 42 -74.91 -73.43
REMARK 500 6 TYR A 49 56.82 -97.93
REMARK 500 6 ARG A 51 79.79 -101.49
REMARK 500 6 SER A 52 -85.58 -107.02
REMARK 500 6 GLU A 67 -145.47 -123.67
REMARK 500 6 GLU A 71 -168.04 -120.53
REMARK 500 7 LYS A 2 -72.20 60.83
REMARK 500 7 LYS A 3 88.27 76.79
REMARK 500 7 VAL A 4 -72.54 -113.97
REMARK 500 7 TRP A 15 154.11 77.83
REMARK 500 7 ASP A 29 -76.56 -166.97
REMARK 500 7 LYS A 31 73.39 51.12
REMARK 500 7 ASN A 44 -49.13 69.53
REMARK 500 7 LEU A 50 -86.83 -82.16
REMARK 500 8 LYS A 3 103.29 -48.45
REMARK 500 8 VAL A 4 103.64 61.90
REMARK 500 8 TRP A 15 -79.29 -69.83
REMARK 500 8 PHE A 16 114.69 75.10
REMARK 500 8 THR A 30 24.59 -146.40
REMARK 500 8 LYS A 31 76.37 67.09
REMARK 500 8 TYR A 49 166.81 75.85
REMARK 500 8 ARG A 51 112.76 71.41
REMARK 500 8 SER A 52 -70.37 -81.23
REMARK 500 9 LYS A 3 -97.16 -79.14
REMARK 500 9 VAL A 4 117.15 65.61
REMARK 500 9 LYS A 14 -99.14 -102.47
REMARK 500 9 ARG A 27 147.65 -36.12
REMARK 500 9 ASP A 29 -78.51 -82.94
REMARK 500 9 LYS A 31 67.53 60.09
REMARK 500 9 ASN A 45 68.58 -118.53
REMARK 500 9 LYS A 48 -93.38 -92.50
REMARK 500 9 LEU A 50 -60.51 74.20
REMARK 500 9 GLU A 67 -136.23 -89.45
REMARK 500 10 LYS A 3 -28.65 -145.78
REMARK 500 10 LYS A 8 73.12 59.05
REMARK 500 10 LYS A 14 -100.69 -95.14
REMARK 500 10 ASP A 29 -72.57 -132.42
REMARK 500 10 ARG A 47 -81.25 -107.54
REMARK 500 10 GLU A 67 -85.26 -80.12
REMARK 500 10 GLU A 71 -166.81 -117.83
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 3 ARG A 27 0.11 SIDE CHAIN
REMARK 500 4 ARG A 27 0.11 SIDE CHAIN
REMARK 500 4 ARG A 51 0.08 SIDE CHAIN
REMARK 500 6 ARG A 27 0.08 SIDE CHAIN
REMARK 500 7 ARG A 27 0.12 SIDE CHAIN
REMARK 500 10 ARG A 19 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 1 ASN A 28 23.1 L L OUTSIDE RANGE
REMARK 500 3 ASN A 74 24.2 L L OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES
REMARK 999 15-92) WHICH REPRESENTS Y-BOX BINDING PROTEIN FROM COLUMBA LIVIA
REMARK 999 (DOMESTIC PIGEON).
REMARK 999 N-TERMINAL METHIONINE ADDED IN PDB-SEQUENCE
DBREF 1H95 A 1 79 PDB 1H95 1H95 1 79
SEQRES 1 A 79 MET LYS LYS VAL ILE ALA THR LYS VAL LEU GLY THR VAL
SEQRES 2 A 79 LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE ASN
SEQRES 3 A 79 ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN THR
SEQRES 4 A 79 ALA ILE LYS LYS ASN ASN PRO ARG LYS TYR LEU ARG SER
SEQRES 5 A 79 VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL GLU
SEQRES 6 A 79 GLY GLU LYS GLY ALA GLU ALA ALA ASN VAL THR GLY PRO
SEQRES 7 A 79 GLY
SHEET 1 AA 6 LYS A 3 VAL A 18 0
SHEET 2 AA 6 GLU A 57 GLU A 65 -1 O VAL A 59 N GLY A 11
SHEET 3 AA 6 GLY A 69 THR A 76 -1 O GLU A 71 N VAL A 64
SHEET 4 AA 6 LYS A 31 HIS A 37 1 O ASP A 33 N ALA A 70
SHEET 5 AA 6 GLY A 21 ASN A 28 -1 O GLY A 23 N VAL A 36
SHEET 6 AA 6 LYS A 3 VAL A 18 -1 O THR A 12 N ASN A 26
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 - r 25 2 Bytes