HEADER HYDROLASE/DNA 16-AUG-09 2KN7
TITLE STRUCTURE OF THE XPF-SINGLE STRAND DNA COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA REPAIR ENDONUCLEASE XPF;
COMPND 3 CHAIN: A, D;
COMPND 4 FRAGMENT: RESIDUES IN UNP 842-908;
COMPND 5 SYNONYM: DNA EXCISION REPAIR PROTEIN ERCC-4, DNA REPAIR PROTEIN
COMPND 6 COMPLEMENTING XP-F CELLS, XERODERMA PIGMENTOSUM GROUP F-COMPLEMENTING
COMPND 7 PROTEIN;
COMPND 8 EC: 3.1.-.-;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3');
COMPND 12 CHAIN: B, C;
COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: XPF;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28B;
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES
KEYWDS NER, XPF/ERCC1, HHH, PROTEIN-SSDNA COMPLEX, HYDROLASE-DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR D.DAS,G.E.FOLKERS,M.VAN DIJK,N.G.J.JASPERS,J.H.J.HOEIJMAKERS,
AUTHOR 2 R.KAPTEIN,R.BOELENS
REVDAT 2 04-JUL-12 2KN7 1 JRNL VERSN
REVDAT 1 04-AUG-10 2KN7 0
JRNL AUTH D.DAS,G.E.FOLKERS,M.VAN DIJK,N.G.J.JASPERS,
JRNL AUTH 2 J.H.J.HOEIJMAKERS,R.KAPTEIN,R.BOELENS
JRNL TITL THE STRUCTURE OF THE XPF-SSDNA COMPLEX UNDERSCORES THE
JRNL TITL 2 DISTINCT ROLES OF THE XPF AND ERCC1 HELIX- HAIRPIN-HELIX
JRNL TITL 3 DOMAINS IN SS/DS DNA RECOGNITION
JRNL REF STRUCTURE V. 20 667 2012
JRNL REFN ISSN 0969-2126
JRNL PMID 22483113
JRNL DOI 10.1016/J.STR.2012.02.009
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2KN7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-09.
REMARK 100 THE RCSB ID CODE IS RCSB101329.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293.8
REMARK 210 PH : 5.2
REMARK 210 IONIC STRENGTH : 80-100
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 80MM SODIUM PHOSPHATE-1, 2MM
REMARK 210 SODIUM CHLORIDE-2, 0.005-0.010MM
REMARK 210 AEBSF PROTEASE INHIBITOR-3, 95%
REMARK 210 H2O/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N
REMARK 210 NOESY; 3D CBCA(CO)NH; 2D 1H-15N
REMARK 210 HSQC; 2D 1H-13C HSQC; 3D HCCH-
REMARK 210 TOCSY; 3D C(CO)NH
REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 3.5, CYANA
REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION
REMARK 210 ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, C
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 ASP D 167 HG1 THR D 171 1.57
REMARK 500 HZ1 LYS D 163 OD2 ASP D 167 1.58
REMARK 500 H2'' DG B 3 O5' DT B 4 1.60
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 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 3 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 3 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 4 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 5 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 5 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 7 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 7 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 8 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 10 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 10 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 11 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 11 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 12 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 12 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 13 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 13 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 15 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 15 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 16 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 16 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 17 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 18 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 18 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 19 DG C 9 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 20 DG B 9 N3 - C2 - N2 ANGL. DEV. = -4.3 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 ASN A 40 -132.37 -173.56
REMARK 500 1 LYS D 111 -70.28 -72.24
REMARK 500 1 TYR D 112 68.19 65.84
REMARK 500 1 PRO D 114 10.81 -68.69
REMARK 500 1 ASN D 140 -132.49 -171.24
REMARK 500 1 GLU D 175 73.57 61.52
REMARK 500 2 PRO A 14 14.66 -67.85
REMARK 500 2 ASN A 40 -133.59 -175.93
REMARK 500 2 LYS D 111 -70.69 -54.79
REMARK 500 2 TYR D 112 81.05 57.21
REMARK 500 2 PRO D 114 14.70 -67.29
REMARK 500 2 ASN D 140 -134.89 -174.63
REMARK 500 3 PRO A 14 12.07 -68.43
REMARK 500 3 ASN A 40 -133.29 -175.94
REMARK 500 3 TYR D 112 105.15 -46.55
REMARK 500 3 PRO D 114 16.77 -68.59
REMARK 500 3 ASN D 140 -137.20 -175.05
REMARK 500 4 PRO A 14 14.16 -69.99
REMARK 500 4 ASN A 40 -126.35 -174.51
REMARK 500 4 TYR D 112 75.81 63.16
REMARK 500 4 PRO D 114 20.03 -68.78
REMARK 500 4 ASN D 140 -135.62 -174.95
REMARK 500 4 GLU D 175 103.87 69.27
REMARK 500 5 PRO A 14 11.24 -69.58
REMARK 500 5 ASN A 40 -134.33 -175.73
REMARK 500 5 LYS D 111 -71.95 -74.65
REMARK 500 5 TYR D 112 100.72 63.11
REMARK 500 5 ASN D 140 -130.64 -174.22
REMARK 500 5 GLU D 175 -174.57 -171.57
REMARK 500 6 TYR A 12 105.01 70.71
REMARK 500 6 ASN A 40 -133.21 -177.42
REMARK 500 6 LYS D 111 -70.26 -74.43
REMARK 500 6 TYR D 112 105.56 64.84
REMARK 500 6 PRO D 114 20.37 -68.44
REMARK 500 6 ASN D 140 -137.01 -176.33
REMARK 500 7 ASN A 40 -128.68 -172.17
REMARK 500 7 LYS D 111 -71.73 -83.69
REMARK 500 7 TYR D 112 92.36 55.32
REMARK 500 7 PRO D 114 22.67 -69.69
REMARK 500 7 ASN D 140 -132.01 -173.94
REMARK 500 7 GLU D 175 -176.64 -175.72
REMARK 500 8 TYR A 12 98.24 -64.42
REMARK 500 8 PRO A 14 10.96 -66.80
REMARK 500 8 ASN A 40 -136.60 -178.57
REMARK 500 8 ASN D 140 -132.60 -175.46
REMARK 500 9 TYR A 12 77.01 57.75
REMARK 500 9 PRO A 14 9.14 -68.01
REMARK 500 9 ASN A 40 -132.73 -175.95
REMARK 500 9 TYR D 112 99.03 -67.92
REMARK 500 9 PRO D 114 11.59 -67.77
REMARK 500
REMARK 500 THIS ENTRY HAS 119 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2AQ0 RELATED DB: PDB
REMARK 900 RELATED ID: 1Z00 RELATED DB: PDB
DBREF 2KN7 A 10 76 UNP Q92889 XPF_HUMAN 842 908
DBREF 2KN7 D 110 176 UNP Q92889 XPF_HUMAN 842 908
DBREF 2KN7 B 1 10 PDB 2KN7 2KN7 1 10
DBREF 2KN7 C 1 10 PDB 2KN7 2KN7 1 10
SEQRES 1 A 67 GLU LYS TYR ASN PRO GLY PRO GLN ASP PHE LEU LEU LYS
SEQRES 2 A 67 MET PRO GLY VAL ASN ALA LYS ASN CYS ARG SER LEU MET
SEQRES 3 A 67 HIS HIS VAL LYS ASN ILE ALA GLU LEU ALA ALA LEU SER
SEQRES 4 A 67 GLN ASP GLU LEU THR SER ILE LEU GLY ASN ALA ALA ASN
SEQRES 5 A 67 ALA LYS GLN LEU TYR ASP PHE ILE HIS THR SER PHE ALA
SEQRES 6 A 67 GLU VAL
SEQRES 1 D 67 GLU LYS TYR ASN PRO GLY PRO GLN ASP PHE LEU LEU LYS
SEQRES 2 D 67 MET PRO GLY VAL ASN ALA LYS ASN CYS ARG SER LEU MET
SEQRES 3 D 67 HIS HIS VAL LYS ASN ILE ALA GLU LEU ALA ALA LEU SER
SEQRES 4 D 67 GLN ASP GLU LEU THR SER ILE LEU GLY ASN ALA ALA ASN
SEQRES 5 D 67 ALA LYS GLN LEU TYR ASP PHE ILE HIS THR SER PHE ALA
SEQRES 6 D 67 GLU VAL
SEQRES 1 B 10 DC DA DG DT DG DG DC DT DG DA
SEQRES 1 C 10 DC DA DG DT DG DG DC DT DG DA
HELIX 1 1 GLY A 15 LYS A 22 1 8
HELIX 2 2 ASN A 27 VAL A 38 1 12
HELIX 3 3 ASN A 40 LEU A 47 1 8
HELIX 4 4 SER A 48 GLY A 57 1 10
HELIX 5 5 ASN A 58 HIS A 70 1 13
HELIX 6 6 GLY D 115 LYS D 122 1 8
HELIX 7 7 ASN D 127 VAL D 138 1 12
HELIX 8 8 ASN D 140 LEU D 147 1 8
HELIX 9 9 SER D 148 GLY D 157 1 10
HELIX 10 10 ASN D 158 HIS D 170 1 13
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
