HEADER DNA BINDING PROTEIN, PROTEIN BINDING 05-SEP-05 2AXL
TITLE SOLUTION STRUCTURE OF A MULTIFUNCTIONAL DNA- AND PROTEIN-BINDING
TITLE 2 DOMAIN OF HUMAN WERNER SYNDROME PROTEIN
CAVEAT 2AXL CHIRALITY ERROR AT THE CG CENTER OF LEU A 115
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: WERNER SYNDROME;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: THE DPBD;
COMPND 5 ENGINEERED: YES
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 BL21;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32D
KEYWDS THE WH-LIKE DOMAIN, DNA BINDING PROTEIN, PROTEIN BINDING
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR J.-S.HU,H.FENG,W.ZENG,G.-X.LIN,X.G.XI
REVDAT 4 09-MAR-22 2AXL 1 REMARK
REVDAT 3 24-FEB-09 2AXL 1 VERSN
REVDAT 2 10-JAN-06 2AXL 1 JRNL
REVDAT 1 13-DEC-05 2AXL 0
JRNL AUTH J.-S.HU,H.FENG,W.ZENG,G.-X.LIN,X.G.XI
JRNL TITL SOLUTION STRUCTURE OF A MULTIFUNCTIONAL DNA- AND
JRNL TITL 2 PROTEIN-BINDING MOTIF OF HUMAN WERNER SYNDROME PROTEIN.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 18379 2005
JRNL REFN ISSN 0027-8424
JRNL PMID 16339893
JRNL DOI 10.1073/PNAS.0509380102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XPLOR-NIH XPLOR-NIH, XPLOR-NIH XPLOR-NIH
REMARK 3 AUTHORS : SCHWIETERS, C.D., KUSZEWSKI, J., TJANDRA, N. &
REMARK 3 CLORE, G.M. (2003) (XPLOR-NIH), SCHWIETERS, C.D.,
REMARK 3 KUSZEWSKI, J., TJANDRA, N. & CLORE, G.M. (2003)
REMARK 3 (XPLOR-NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2AXL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-05.
REMARK 100 THE DEPOSITION ID IS D_1000034434.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 295.2
REMARK 210 PH : 7.4
REMARK 210 IONIC STRENGTH : 25 MM KPI + 25 MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.35 MM IN KPI BUFFER (PH7.4) 25
REMARK 210 MM NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : D_15N-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; 4D_13C-
REMARK 210 SEPARATED_NOESY; 4D_13C/15N-
REMARK 210 SEPARATED_NOESY; HNHA; HNCG_AROM,
REMARK 210 HN(CO)CG_AROM
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 : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION
REMARK 210 ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM,
REMARK 210 STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: HCCH-COSY WAS OPTIMIZED FOR DETECTION FOR CH3 GROUPS,
REMARK 210 2D SPIN ECHO FOR 1H-13C HSQC SELECTED FOR AROMATIC AND CARBONYL
REMARK 210 CONTAINING RESIDUES
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 HG1 THR A 7 OG SER A 8 1.25
REMARK 500 HE22 GLN A 14 HE1 TRP A 66 1.30
REMARK 500 O SER A 65 H ALA A 69 1.41
REMARK 500 O PHE A 16 H SER A 20 1.42
REMARK 500 O ALA A 15 H LEU A 19 1.52
REMARK 500 O THR A 96 H ARG A 100 1.53
REMARK 500 O ARG A 100 H HIS A 104 1.54
REMARK 500 HE1 TRP A 9 O GLN A 116 1.58
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 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 1 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 1 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 1 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 1 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 2 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 2 PHE A 37 CA - C - N ANGL. DEV. = 25.0 DEGREES
REMARK 500 2 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 2 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 2 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 3 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 3 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 3 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 3 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 3 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 4 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 4 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 4 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 4 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 4 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.9 DEGREES
REMARK 500 5 PHE A 37 CA - C - O ANGL. DEV. = -24.1 DEGREES
REMARK 500 5 PHE A 37 CA - C - N ANGL. DEV. = 25.0 DEGREES
REMARK 500 5 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 5 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 5 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 6 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 6 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 6 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 6 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 6 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 7 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 7 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 7 ILE A 114 N - CA - C ANGL. DEV. = -18.6 DEGREES
REMARK 500 7 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 7 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 8 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 8 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 8 ILE A 114 N - CA - C ANGL. DEV. = -18.5 DEGREES
REMARK 500 8 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.3 DEGREES
REMARK 500 8 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 DEGREES
REMARK 500 9 PHE A 37 CA - C - O ANGL. DEV. = -24.2 DEGREES
REMARK 500 9 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 9 ILE A 114 N - CA - C ANGL. DEV. = -18.5 DEGREES
REMARK 500 9 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 9 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.9 DEGREES
REMARK 500 10 PHE A 37 CA - C - O ANGL. DEV. = -24.1 DEGREES
REMARK 500 10 PHE A 37 CA - C - N ANGL. DEV. = 25.1 DEGREES
REMARK 500 10 ILE A 114 N - CA - C ANGL. DEV. = -18.5 DEGREES
REMARK 500 10 LEU A 115 CB - CG - CD1 ANGL. DEV. = 40.4 DEGREES
REMARK 500 10 LEU A 115 CB - CG - CD2 ANGL. DEV. = -64.8 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 ASP A 6 -161.98 -77.90
REMARK 500 1 SER A 8 118.05 -171.37
REMARK 500 1 TRP A 9 132.75 178.70
REMARK 500 1 GLU A 27 3.15 55.24
REMARK 500 1 LYS A 28 39.38 -81.54
REMARK 500 1 TYR A 50 35.12 -95.29
REMARK 500 1 HIS A 53 101.28 -42.89
REMARK 500 1 ASN A 87 91.81 87.06
REMARK 500 1 PHE A 89 -77.22 -74.65
REMARK 500 1 MET A 90 87.40 -159.56
REMARK 500 1 LYS A 91 91.76 28.37
REMARK 500 1 THR A 96 -166.99 -100.46
REMARK 500 1 THR A 108 -92.85 -77.54
REMARK 500 1 LEU A 113 112.89 -172.36
REMARK 500 1 CYS A 122 71.10 -155.68
REMARK 500 1 LYS A 125 34.29 -82.19
REMARK 500 1 LYS A 139 107.83 -165.36
REMARK 500 2 SER A 4 103.44 -58.51
REMARK 500 2 TRP A 9 144.89 -176.32
REMARK 500 2 LYS A 28 40.15 -82.37
REMARK 500 2 TYR A 50 1.90 -65.53
REMARK 500 2 LEU A 55 8.61 -56.04
REMARK 500 2 ASN A 87 82.85 84.61
REMARK 500 2 PHE A 89 -81.53 -77.81
REMARK 500 2 LYS A 91 97.63 30.64
REMARK 500 2 ALA A 106 -1.65 -57.60
REMARK 500 2 THR A 108 -95.36 -50.56
REMARK 500 2 LYS A 139 108.59 -164.27
REMARK 500 2 GLU A 140 34.21 -99.66
REMARK 500 3 TRP A 9 140.83 -178.64
REMARK 500 3 SER A 43 97.88 -162.47
REMARK 500 3 TYR A 50 36.54 -83.70
REMARK 500 3 HIS A 53 89.62 -42.30
REMARK 500 3 LEU A 55 -2.30 -50.10
REMARK 500 3 ASN A 87 91.56 87.57
REMARK 500 3 PHE A 89 -80.94 -75.83
REMARK 500 3 LYS A 91 91.70 26.95
REMARK 500 3 LYS A 97 -17.30 -46.70
REMARK 500 3 LYS A 105 -51.06 -136.82
REMARK 500 3 ALA A 106 30.29 -83.30
REMARK 500 3 THR A 108 -99.35 -75.35
REMARK 500 3 GLU A 109 71.34 -150.37
REMARK 500 3 LEU A 121 55.14 -106.31
REMARK 500 3 CYS A 122 62.41 -150.82
REMARK 500 3 LYS A 125 57.14 -67.50
REMARK 500 3 LYS A 139 108.83 -166.25
REMARK 500 4 SER A 4 96.34 -58.85
REMARK 500 4 SER A 8 116.28 -166.52
REMARK 500 4 TRP A 9 140.42 177.28
REMARK 500 4 ARG A 39 6.77 -62.98
REMARK 500
REMARK 500 THIS ENTRY HAS 170 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2AXL A 1 144 UNP Q14191 WRN_HUMAN 949 1092
SEQRES 1 A 144 MET ASP ASP SER GLU ASP THR SER TRP ASP PHE GLY PRO
SEQRES 2 A 144 GLN ALA PHE LYS LEU LEU SER ALA VAL ASP ILE LEU GLY
SEQRES 3 A 144 GLU LYS PHE GLY ILE GLY LEU PRO ILE LEU PHE LEU ARG
SEQRES 4 A 144 GLY SER ASN SER GLN ARG LEU ALA ASP GLN TYR ARG ARG
SEQRES 5 A 144 HIS SER LEU PHE GLY THR GLY LYS ASP GLN THR GLU SER
SEQRES 6 A 144 TRP TRP LYS ALA PHE SER ARG GLN LEU ILE THR GLU GLY
SEQRES 7 A 144 PHE LEU VAL GLU VAL SER ARG TYR ASN LYS PHE MET LYS
SEQRES 8 A 144 ILE CYS ALA LEU THR LYS LYS GLY ARG ASN TRP LEU HIS
SEQRES 9 A 144 LYS ALA ASN THR GLU SER GLN SER LEU ILE LEU GLN ALA
SEQRES 10 A 144 ASN GLU GLU LEU CYS PRO LYS LYS LEU LEU LEU PRO SER
SEQRES 11 A 144 SER LYS THR VAL SER SER GLY THR LYS GLU HIS CYS TYR
SEQRES 12 A 144 ASN
HELIX 1 1 PHE A 11 LEU A 25 1 15
HELIX 2 2 ILE A 31 ARG A 39 1 9
HELIX 3 3 GLN A 44 TYR A 50 1 7
HELIX 4 4 GLY A 57 GLN A 62 5 6
HELIX 5 5 THR A 63 GLY A 78 1 16
HELIX 6 6 THR A 96 ALA A 106 1 11
SHEET 1 A 2 SER A 8 ASP A 10 0
SHEET 2 A 2 ILE A 114 GLN A 116 -1 O LEU A 115 N TRP A 9
SHEET 1 B 2 LEU A 80 VAL A 83 0
SHEET 2 B 2 ILE A 92 LEU A 95 -1 O ALA A 94 N VAL A 81
CISPEP 1 THR A 7 SER A 8 1 -7.94
CISPEP 2 THR A 7 SER A 8 2 -7.74
CISPEP 3 THR A 7 SER A 8 3 -7.62
CISPEP 4 THR A 7 SER A 8 4 -7.44
CISPEP 5 THR A 7 SER A 8 5 -7.46
CISPEP 6 THR A 7 SER A 8 6 -7.27
CISPEP 7 THR A 7 SER A 8 7 -7.32
CISPEP 8 THR A 7 SER A 8 8 -7.20
CISPEP 9 THR A 7 SER A 8 9 -8.18
CISPEP 10 THR A 7 SER A 8 10 -7.37
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
(ATOM LINES ARE NOT SHOWN.)
END