HEADER NUCLEOTIDYLTRANSFERASE 25-OCT-94 1RPL TITLE 2.3 ANGSTROMS CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA TITLE 2 POLYMERASE BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.F.DAVIES II,R.J.ALMASSY REVDAT 5 14-FEB-24 1RPL 1 REMARK REVDAT 4 29-NOV-17 1RPL 1 HELIX REVDAT 3 24-FEB-09 1RPL 1 VERSN REVDAT 2 01-APR-03 1RPL 1 JRNL REVDAT 1 26-JAN-95 1RPL 0 JRNL AUTH J.F.DAVIES 2ND.,R.J.ALMASSY,Z.HOSTOMSKA,R.A.FERRE, JRNL AUTH 2 Z.HOSTOMSKY JRNL TITL 2.3 A CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA JRNL TITL 2 POLYMERASE BETA. JRNL REF CELL(CAMBRIDGE,MASS.) V. 76 1123 1994 JRNL REFN ISSN 0092-8674 JRNL PMID 8137427 JRNL DOI 10.1016/0092-8674(94)90388-3 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12020 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 BOND ANGLES (DEGREES) : 3.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 60.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.70000 REMARK 290 SMTRY3 4 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: 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 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 LEU A 85 REMARK 465 GLU A 86 REMARK 465 LYS A 87 REMARK 465 ILE A 88 REMARK 465 ARG A 89 REMARK 465 GLN A 90 REMARK 465 ASP A 91 REMARK 465 ASP A 92 REMARK 465 THR A 93 REMARK 465 SER A 94 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 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LYS A 141 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 TYR A 173 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LEU A 195 CA - CB - CG ANGL. DEV. = 18.2 DEGREES REMARK 500 LYS A 206 N - CA - C ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR A 250 CA - CB - CG ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 254 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 254 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR A 266 CA - CB - CG ANGL. DEV. = -12.4 DEGREES REMARK 500 GLY A 274 CA - C - N ANGL. DEV. = -20.6 DEGREES REMARK 500 GLY A 274 O - C - N ANGL. DEV. = 12.3 DEGREES REMARK 500 SER A 275 C - N - CA ANGL. DEV. = 22.5 DEGREES REMARK 500 ARG A 299 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 326 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 328 CA - CB - CG ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG A 333 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ILE A 97 47.06 -76.82 REMARK 500 ASN A 98 -41.10 -151.86 REMARK 500 GLU A 117 16.73 -62.00 REMARK 500 ASN A 128 32.45 -140.56 REMARK 500 ASP A 170 113.68 -170.96 REMARK 500 CYS A 178 -142.03 -90.52 REMARK 500 GLU A 203 42.54 -105.83 REMARK 500 LYS A 206 -52.62 -23.54 REMARK 500 GLU A 244 33.89 37.30 REMARK 500 ASN A 245 -147.39 -165.73 REMARK 500 ASP A 246 67.48 -69.35 REMARK 500 GLU A 247 -17.53 62.52 REMARK 500 ASN A 248 171.94 51.74 REMARK 500 GLU A 249 45.42 -70.67 REMARK 500 SER A 275 121.50 120.38 REMARK 500 THR A 304 -133.16 -166.21 REMARK 500 VAL A 306 91.53 -67.47 REMARK 500 ARG A 333 42.67 -100.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 1RPL A 85 335 UNP P06766 DPOB_RAT 84 334 SEQRES 1 A 251 LEU GLU LYS ILE ARG GLN ASP ASP THR SER SER SER ILE SEQRES 2 A 251 ASN PHE LEU THR ARG VAL THR GLY ILE GLY PRO SER ALA SEQRES 3 A 251 ALA ARG LYS LEU VAL ASP GLU GLY ILE LYS THR LEU GLU SEQRES 4 A 251 ASP LEU ARG LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN SEQRES 5 A 251 ARG ILE GLY LEU LYS TYR PHE GLU ASP PHE GLU LYS ARG SEQRES 6 A 251 ILE PRO ARG GLU GLU MET LEU GLN MET GLN ASP ILE VAL SEQRES 7 A 251 LEU ASN GLU VAL LYS LYS LEU ASP PRO GLU TYR ILE ALA SEQRES 8 A 251 THR VAL CYS GLY SER PHE ARG ARG GLY ALA GLU SER SER SEQRES 9 A 251 GLY ASP MET ASP VAL LEU LEU THR HIS PRO ASN PHE THR SEQRES 10 A 251 SER GLU SER SER LYS GLN PRO LYS LEU LEU HIS ARG VAL SEQRES 11 A 251 VAL GLU GLN LEU GLN LYS VAL ARG PHE ILE THR ASP THR SEQRES 12 A 251 LEU SER LYS GLY GLU THR LYS PHE MET GLY VAL CYS GLN SEQRES 13 A 251 LEU PRO SER GLU ASN ASP GLU ASN GLU TYR PRO HIS ARG SEQRES 14 A 251 ARG ILE ASP ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR SEQRES 15 A 251 CYS GLY VAL LEU TYR PHE THR GLY SER ASP ILE PHE ASN SEQRES 16 A 251 LYS ASN MET ARG ALA HIS ALA LEU GLU LYS GLY PHE THR SEQRES 17 A 251 ILE ASN GLU TYR THR ILE ARG PRO LEU GLY VAL THR GLY SEQRES 18 A 251 VAL ALA GLY GLU PRO LEU PRO VAL ASP SER GLU GLN ASP SEQRES 19 A 251 ILE PHE ASP TYR ILE GLN TRP ARG TYR ARG GLU PRO LYS SEQRES 20 A 251 ASP ARG SER GLU FORMUL 2 HOH *59(H2 O) HELIX 1 A SER A 96 ARG A 102 1 7 HELIX 2 B GLY A 107 GLU A 117 1 11 HELIX 3 C THR A 121 ASN A 128 1 8 HELIX 4 D ASN A 133 TYR A 142 1 10 HELIX 5 E TYR A 142 PHE A 146 1 5 HELIX 6 F ARG A 152 ASP A 170 1 19 HELIX 7 G SER A 180 GLY A 184 1 5 HELIX 8 H PRO A 208 VAL A 221 1 14 HELIX 9 I GLN A 264 GLY A 274 1 11 HELIX 10 J ASP A 276 GLY A 290 1 15 HELIX 11 K GLU A 316 GLN A 324 1 9 HELIX 12 310 GLU A 329 ARG A 333 5 5 SHEET 1 S1 5 ILE A 174 CYS A 178 0 SHEET 2 S1 5 MET A 191 THR A 196 -1 SHEET 3 S1 5 ARG A 253 ILE A 260 1 SHEET 4 S1 5 THR A 233 CYS A 239 -1 SHEET 5 S1 5 ILE A 224 GLY A 231 -1 CRYST1 120.800 63.400 38.700 90.00 90.00 90.00 P 21 21 2 4 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 0.008278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025840 0.00000