HEADER TRANSLATION FACTOR 23-FEB-01 1H95 TITLE SOLUTION STRUCTURE OF THE SINGLE-STRANDED DNA-BINDING COLD SHOCK TITLE 2 DOMAIN (CSD) OF HUMAN Y-BOX PROTEIN 1 (YB1) DETERMINED BY NMR (10 TITLE 3 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 DOMAIN(CSD) OF COMPND 8 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-STRANDED ANTI- KEYWDS 2 PARALLEL BETA-BARREL, SINGLE STRANDED DNA 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,S.GRZESIEK, AUTHOR 2 C.W.HILBERS REVDAT 3 15-MAY-24 1H95 1 REMARK 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 OF THE JRNL TITL 2 COLD-SHOCK DOMAIN OF THE HUMAN Y-BOX 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 : 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 23-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1290005936. 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; 15N-EDITED REMARK 210 ROESY; 13C-EDITED NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, PIPP, X-PLOR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS FOLLOWED REMARK 210 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 NMR REMARK 210 SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK DOMAIN OF REMARK 210 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 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 REMARK 500 REMARK: NULL 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 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 VAL A 53 -77.88 -128.27 REMARK 500 1 GLU A 67 -71.23 -100.35 REMARK 500 1 GLU A 71 -162.86 -122.37 REMARK 500 1 THR A 76 -134.27 -96.32 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 2 THR A 76 -121.85 -125.96 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 4 THR A 76 -122.09 -113.52 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 65 -111.29 -139.95 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 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. 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 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4147 RELATED DB: BMRB 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 HELIX 1 1 THR A 39 ILE A 41 5 3 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