10 20 30 40 50 60 70 80 1BPZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER TRANSFERASE/DNA 14-APR-97 1BPZ
TITLE HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: PROTEIN (DNA POLYMERASE BETA); COMPND 16 CHAIN: A; COMPND 17 SYNONYM: POL BETA, BETA-POL; COMPND 18 EC: 2.7.7.7; COMPND 19 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 CELLULAR_LOCATION: NUCLEUS; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS NUCLEOTIDYLTRANSFERASE, DNA REPAIR, BASE EXCISION REPAIR KEYWDS 2 PATHWAY, TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.R.SAWAYA,R.PRASAD,S.H.WILSON,J.KRAUT,H.PELLETIER
REVDAT 3 24-FEB-09 1BPZ 1 VERSN REVDAT 2 03-FEB-04 1BPZ 1 JRNL LINK REVDAT 1 16-JUN-97 1BPZ 0
JRNL AUTH M.R.SAWAYA,R.PRASAD,S.H.WILSON,J.KRAUT,H.PELLETIER JRNL TITL CRYSTAL STRUCTURES OF HUMAN DNA POLYMERASE BETA JRNL TITL 2 COMPLEXED WITH GAPPED AND NICKED DNA: EVIDENCE FOR JRNL TITL 3 AN INDUCED FIT MECHANISM. JRNL REF BIOCHEMISTRY V. 36 11205 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9287163 JRNL DOI 10.1021/BI9703812
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA REMARK 1 TITL CHARACTERIZATION OF THE METAL ION BINDING REMARK 1 TITL 2 HELIX-HAIRPIN-HELIX MOTIFS IN HUMAN DNA POLYMERASE REMARK 1 TITL 3 BETA BY X-RAY STRUCTURAL ANALYSIS REMARK 1 REF BIOCHEMISTRY V. 35 12778 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,W.WOLFLE,S.H.WILSON,J.KRAUT REMARK 1 TITL A STRUCTURAL BASIS FOR METAL ION MUTAGENICITY AND REMARK 1 TITL 2 NUCLEOTIDE SELECTIVITY IN HUMAN DNA POLYMERASE BETA REMARK 1 REF BIOCHEMISTRY V. 35 12762 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,W.WOLFLE,S.H.WILSON,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF HUMAN DNA POLYMERASE BETA REMARK 1 TITL 2 COMPLEXED WITH DNA: IMPLICATIONS FOR CATALYTIC REMARK 1 TITL 3 MECHANISM, PROCESSIVITY, AND FIDELITY REMARK 1 REF BIOCHEMISTRY V. 35 12742 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: REMARK 1 TITL 2 EVIDENCE FOR A COMMON POLYMERASE MECHANISM REMARK 1 REF SCIENCE V. 264 1930 1994 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 5 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,A.KUMAR,S.H.WILSON,J.KRAUT REMARK 1 TITL STRUCTURES OF TERNARY COMPLEXES OF RAT DNA REMARK 1 TITL 2 POLYMERASE BETA, A DNA TEMPLATE- PRIMER, AND DDCTP REMARK 1 REF SCIENCE V. 264 1891 1994 REMARK 1 REFN ISSN 0036-8075
REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT V. 5-D REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 14702 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2430 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14702 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2653 REMARK 3 NUCLEIC ACID ATOMS : 651 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.020 ; 0.550 ; 3474 REMARK 3 BOND ANGLES (DEGREES) : 3.000 ; 1.000 ; 4754 REMARK 3 TORSION ANGLES (DEGREES) : 22.200; 1.000 ; 2027 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.013 ; 1.000 ; 74 REMARK 3 GENERAL PLANES (A) : 0.007 ; 10.000; 432 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 7.000 ; 0.025 ; 3474 REMARK 3 NON-BONDED CONTACTS (A) : 0.022 ; 10.000; 270 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MOEWS REMARK 3 KSOL : 0.71 REMARK 3 BSOL : 88.70 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTIRE THUMB SUBDOMAIN (RESIDUES REMARK 3 261 - 335) IS MODELED WITH ONLY 0.5 OCCUPANCY DUE TO WEAK REMARK 3 ELECTRON DENSITY. THERE IS NO OTHER PATTERN OF DENSITY REMARK 3 WARRANTING A SECOND POSITION FOR THE THUMB SUBDOMAIN.
REMARK 4 REMARK 4 1BPZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 100.00 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34400 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 9ICJ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN-DNA COMPLEX WAS REMARK 280 CRYSTALLIZED USING A RESERVOIR CONTAINING 17.5% PEG 3350, 90 REMARK 280 MM SODIUM ACETATE, AND 50 MM IMIDAZOLE, PH 7.0., VAPOR REMARK 280 DIFFUSION
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.32800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
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: T, P, D, 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 400 REMARK 400 COMPOUND REMARK 400 THE 5'-TERMINUS OF G D 1 IS PHOSPHORYLATED.
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4
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 DG T 3 C5 DG T 3 N7 0.038 REMARK 500 DA T 4 C5' DA T 4 C4' 0.043 REMARK 500 DA T 4 N7 DA T 4 C8 0.065 REMARK 500 DA T 4 C6 DA T 4 N6 0.061 REMARK 500 DC T 5 O4' DC T 5 C1' -0.077 REMARK 500 DC T 5 N1 DC T 5 C6 -0.054 REMARK 500 DC T 5 N3 DC T 5 C4 -0.056 REMARK 500 DC T 5 C4 DC T 5 C5 -0.054 REMARK 500 DA T 7 O3' DA T 7 C3' -0.046 REMARK 500 DA T 11 O4' DA T 11 C4' -0.076 REMARK 500 DA T 14 O3' DA T 14 C3' -0.073 REMARK 500 DG T 15 C5' DG T 15 C4' 0.048 REMARK 500 DG T 15 N3 DG T 15 C4 -0.083 REMARK 500 DC T 16 N3 DC T 16 C4 -0.043 REMARK 500 DG P 1 C5 DG P 1 C6 -0.084 REMARK 500 DG P 1 C5 DG P 1 N7 -0.042 REMARK 500 DG P 1 N9 DG P 1 C4 -0.065 REMARK 500 DG P 4 C5 DG P 4 N7 0.039 REMARK 500 DA P 5 C5 DA P 5 C6 0.055 REMARK 500 DA P 5 C5 DA P 5 N7 0.044 REMARK 500 DG P 7 O3' DG P 7 C3' -0.089 REMARK 500 DG P 9 C2 DG P 9 N3 0.052 REMARK 500 DG P 9 C5 DG P 9 N7 0.067 REMARK 500 DT P 10 C4 DT P 10 C5 -0.089 REMARK 500 DG D 1 P DG D 1 OP3 -0.122 REMARK 500 DG D 1 O3' DG D 1 C3' 0.089 REMARK 500 DG D 1 C4 DG D 1 C5 -0.051 REMARK 500 DG D 1 C5 DG D 1 N7 0.052 REMARK 500 DC D 3 C5' DC D 3 C4' 0.049 REMARK 500 DC D 3 O3' DC D 3 C3' -0.048 REMARK 500 DG D 4 N7 DG D 4 C8 0.052 REMARK 500 DG D 5 N7 DG D 5 C8 0.043 REMARK 500 GLU A 9 CB GLU A 9 CG 0.130 REMARK 500 GLU A 21 CD GLU A 21 OE1 0.067 REMARK 500 GLU A 58 CD GLU A 58 OE1 0.112 REMARK 500 GLU A 71 CD GLU A 71 OE2 0.077 REMARK 500 GLU A 86 CD GLU A 86 OE1 0.066 REMARK 500 GLU A 129 CD GLU A 129 OE2 0.080 REMARK 500 GLU A 147 CD GLU A 147 OE2 0.079 REMARK 500 GLU A 153 CD GLU A 153 OE2 0.068 REMARK 500 GLU A 154 CD GLU A 154 OE2 0.075 REMARK 500 GLU A 165 CD GLU A 165 OE2 0.067 REMARK 500 GLU A 172 CD GLU A 172 OE2 0.071 REMARK 500 GLU A 203 CD GLU A 203 OE1 0.071 REMARK 500 GLU A 232 CD GLU A 232 OE2 0.075 REMARK 500 GLU A 335 CD GLU A 335 OE2 0.066 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 DC T 1 O4' - C1' - N1 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC T 1 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC T 2 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 DC T 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC T 2 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC T 2 C3' - O3' - P ANGL. DEV. = 13.1 DEGREES REMARK 500 DA T 4 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA T 4 C5 - C6 - N1 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC T 5 N1 - C1' - C2' ANGL. DEV. = 10.1 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC T 5 C6 - N1 - C2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC T 5 N1 - C2 - N3 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC T 5 N1 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA T 7 C8 - N9 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC T 8 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC T 8 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DG T 9 N9 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG T 9 C6 - C5 - N7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC T 10 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 DC T 10 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC T 10 N3 - C4 - C5 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA T 11 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA T 11 N7 - C8 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA T 11 C8 - N9 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA T 11 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC T 10 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DC T 13 N1 - C1' - C2' ANGL. DEV. = 12.3 DEGREES REMARK 500 DA T 14 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DA T 14 N7 - C8 - N9 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA T 14 C8 - N9 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG T 15 C5' - C4' - C3' ANGL. DEV. = 7.5 DEGREES REMARK 500 DC T 16 P - O5' - C5' ANGL. DEV. = -9.9 DEGREES REMARK 500 DC T 16 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC T 16 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC T 16 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC T 16 N3 - C4 - N4 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC T 16 C5 - C4 - N4 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG P 1 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES REMARK 500 DG P 1 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG P 1 C2 - N3 - C4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG P 1 N3 - C4 - C5 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG P 1 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC P 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT P 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG P 4 C8 - N9 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA P 5 P - O5' - C5' ANGL. DEV. = -11.1 DEGREES REMARK 500 DA P 5 N9 - C1' - C2' ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 126 ANGLE DEVIATIONS. 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 PRO A 7 -82.74 -85.10 REMARK 500 GLN A 8 -5.63 47.31 REMARK 500 GLU A 9 -76.42 -73.94 REMARK 500 LEU A 11 -87.17 -77.96 REMARK 500 LYS A 27 -81.13 -55.96 REMARK 500 GLN A 31 35.68 80.12 REMARK 500 ALA A 32 79.67 -104.18 REMARK 500 ALA A 38 -71.15 -61.09 REMARK 500 ALA A 42 -78.73 -50.66 REMARK 500 TYR A 49 105.16 -53.17 REMARK 500 PRO A 50 47.07 -58.48 REMARK 500 LYS A 81 -161.94 -160.08 REMARK 500 GLU A 117 21.76 -68.02 REMARK 500 LYS A 120 12.09 -163.64 REMARK 500 LYS A 127 32.53 -86.55 REMARK 500 ASN A 128 13.49 -160.96 REMARK 500 GLU A 129 -18.84 -39.72 REMARK 500 LYS A 131 33.31 -91.39 REMARK 500 LYS A 141 -93.47 -58.97 REMARK 500 TYR A 142 31.57 -60.80 REMARK 500 PHE A 143 -74.40 -45.50 REMARK 500 ARG A 152 -28.67 -30.24 REMARK 500 THR A 176 119.52 -163.55 REMARK 500 ARG A 183 44.98 -80.64 REMARK 500 ALA A 185 156.75 -45.83 REMARK 500 SER A 187 102.83 179.45 REMARK 500 SER A 202 -84.03 -38.19 REMARK 500 GLU A 203 0.26 -64.60 REMARK 500 VAL A 221 38.94 -81.00 REMARK 500 HIS A 222 22.95 41.60 REMARK 500 THR A 225 -81.52 -83.61 REMARK 500 SER A 229 157.48 179.16 REMARK 500 PRO A 242 103.40 -52.66 REMARK 500 TYR A 250 -170.32 -63.03 REMARK 500 TYR A 265 -84.98 -61.33 REMARK 500 TYR A 266 -47.85 -27.30 REMARK 500 THR A 273 -18.22 -47.85 REMARK 500 ASN A 294 -149.60 -161.05 REMARK 500 GLU A 309 99.08 67.38 REMARK 500 SER A 315 148.58 175.02 REMARK 500 TYR A 327 94.09 -56.35 REMARK 500 ARG A 333 35.73 -86.26 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: (11X,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 GLN A 8 22.3 L L OUTSIDE RANGE REMARK 500 GLU A 9 13.0 L L OUTSIDE RANGE REMARK 500 GLN A 31 23.9 L L OUTSIDE RANGE REMARK 500 ARG A 40 21.3 L L OUTSIDE RANGE REMARK 500 LYS A 41 21.6 L L OUTSIDE RANGE REMARK 500 GLU A 86 14.9 L L OUTSIDE RANGE REMARK 500 SER A 109 24.4 L L OUTSIDE RANGE REMARK 500 GLU A 129 19.8 L L OUTSIDE RANGE REMARK 500 ASP A 145 22.9 L L OUTSIDE RANGE REMARK 500 PHE A 146 20.5 L L OUTSIDE RANGE REMARK 500 ASN A 164 5.8 L D EXPECTING SP3 REMARK 500 VAL A 169 24.6 L L OUTSIDE RANGE REMARK 500 SER A 187 21.9 L L OUTSIDE RANGE REMARK 500 LYS A 206 20.7 L L OUTSIDE RANGE REMARK 500 GLN A 207 20.8 L L OUTSIDE RANGE REMARK 500 VAL A 214 20.1 L L OUTSIDE RANGE REMARK 500 HIS A 222 20.5 L L OUTSIDE RANGE REMARK 500 ASP A 226 24.7 L L OUTSIDE RANGE REMARK 500 LYS A 230 23.5 L L OUTSIDE RANGE REMARK 500 THR A 233 22.6 L L OUTSIDE RANGE REMARK 500 GLN A 240 24.3 L L OUTSIDE RANGE REMARK 500 SER A 243 24.2 L L OUTSIDE RANGE REMARK 500 LYS A 248 22.3 L L OUTSIDE RANGE REMARK 500 LYS A 262 21.9 L L OUTSIDE RANGE REMARK 500 GLN A 264 23.5 L L OUTSIDE RANGE REMARK 500 PHE A 272 21.7 L L OUTSIDE RANGE REMARK 500 ASN A 281 24.8 L L OUTSIDE RANGE REMARK 500 ASP A 314 24.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 341 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 THR A 101 O 151.7 REMARK 620 3 HOH A 500 O 78.1 76.1 REMARK 620 4 ILE A 106 O 86.2 119.1 164.3 REMARK 620 5 VAL A 103 O 89.4 78.4 88.1 91.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 342 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 81.0 REMARK 620 3 VAL A 65 O 99.3 89.0 REMARK 620 4 HOH A 502 O 105.7 63.7 138.6 REMARK 620 5 DC D 3 OP1 152.9 74.2 69.9 72.9 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 341 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 342
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BPX RELATED DB: PDB REMARK 900 RELATED ID: 1BPY RELATED DB: PDB
DBREF 1BPZ A 2 335 UNP P06746 DPOB_HUMAN 1 334 DBREF 1BPZ T 1 16 PDB 1BPZ 1BPZ 1 16 DBREF 1BPZ P 1 11 PDB 1BPZ 1BPZ 1 11 DBREF 1BPZ D 1 5 PDB 1BPZ 1BPZ 1 5
SEQRES 1 T 16 DC DC DG DA DC DC DA DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DT DG SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU
HET NA A 341 1 HET NA A 342 1
HETNAM NA SODIUM ION
FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *27(H2 O)
HELIX 1 A GLY A 13 SER A 30 1 18 HELIX 2 B ILE A 33 LYS A 48 1 16 HELIX 3 C GLY A 56 LYS A 61 1 6 HELIX 4 D THR A 67 THR A 79 1SEE REMARK 650 13 HELIX 5 E ARG A 83 GLN A 90 1 8 HELIX 6 F ASP A 92 ARG A 102 1 11 HELIX 7 G PRO A 108 ASP A 116 1SEE REMARK 650 9 HELIX 8 H LEU A 122 LYS A 127 1 6 HELIX 9 I HIS A 134 GLU A 147 1 14 HELIX 10 J ARG A 152 VAL A 169 1 18 HELIX 11 K SER A 180 ARG A 183 1 4 HELIX 12 L PRO A 208 LYS A 220 1 13 HELIX 13 M LYS A 262 THR A 273 1 12 HELIX 14 N ASP A 276 GLU A 288 1 13 HELIX 15 O GLU A 316 ILE A 323 1 8 HELIX 16 P PRO A 330 ASP A 332 5 3
SHEET 1 S1 2 ILE A 150 PRO A 151 0 SHEET 2 S1 2 SER A 187 SER A 188 -1 N SER A 188 O ILE A 150 SHEET 1 S2 5 ILE A 174 CYS A 178 0 SHEET 2 S2 5 MET A 191 THR A 196 -1 N THR A 196 O ILE A 174 SHEET 3 S2 5 ARG A 253 ARG A 258 1 N ASP A 256 O MET A 191 SHEET 4 S2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 S2 5 SER A 229 GLY A 231 -1 O SER A 229 N MET A 236 SHEET 1 S3 2 PHE A 291 ASN A 294 0 SHEET 2 S3 2 THR A 297 PRO A 300 -1 N ARG A 299 O THR A 292
LINK NA NA A 341 OP1 DG P 9 1555 1555 2.43 LINK NA NA A 341 O THR A 101 1555 1555 2.22 LINK NA NA A 341 O HOH A 500 1555 1555 2.19 LINK NA NA A 341 O ILE A 106 1555 1555 2.09 LINK NA NA A 342 O LYS A 60 1555 1555 2.28 LINK NA NA A 342 O LEU A 62 1555 1555 2.23 LINK NA NA A 342 O VAL A 65 1555 1555 2.46 LINK NA NA A 342 O HOH A 502 1555 1555 2.10 LINK OP1 DC D 3 NA NA A 342 1555 1555 2.94 LINK O VAL A 103 NA NA A 341 1555 1555 2.72
CISPEP 1 GLY A 274 SER A 275 0 0.48
SITE 1 ACT 3 ASP A 190 ASP A 192 ASP A 256 SITE 1 AC1 5 THR A 101 VAL A 103 ILE A 106 HOH A 500 SITE 2 AC1 5 DG P 9 SITE 1 AC2 5 LYS A 60 LEU A 62 VAL A 65 HOH A 502 SITE 2 AC2 5 DC D 3
CRYST1 53.535 78.656 54.618 90.00 107.54 90.00 P 1 21 1 2
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 0.018679 0.000000 0.005904 0.00000
SCALE2 0.000000 0.012714 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019202 0.00000