PDB Short entry for 1JN3 HEADER TRANSFERASE 22-JUL-01 1JN3 TITLE FIDELITY PROPERTIES AND STRUCTURE OF M282L MUTATOR MUTANT OF DNA TITLE 2 POLYMERASE: SUBTLE STRUCTURAL CHANGES INFLUENCE THE MECHANISM OF TITLE 3 NUCLEOTIDE DISCRIMINATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 85 - 335; COMPND 5 SYNONYM: BETANUCLEOTIDYLTRANSFERASE; BETA POLYMERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 DNA POLYMERASE BETA (FRAGMENT), MUTANT, NUCLEOTIDE DISCRIMINATION, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.CONN,J.B.SWEASY,J.JAEGER REVDAT 6 07-FEB-24 1JN3 1 REMARK REVDAT 5 27-OCT-21 1JN3 1 SEQADV REVDAT 4 16-NOV-11 1JN3 1 VERSN HETATM REVDAT 3 24-FEB-09 1JN3 1 VERSN REVDAT 2 15-FEB-05 1JN3 1 JRNL REMARK REVDAT 1 03-AUG-01 1JN3 0 JRNL AUTH A.M.SHAH,D.A.CONN,S.-X.LI,A.CAPALDI,J.JAEGER,J.B.SWEASY JRNL TITL A DNA POLYMERASE BETA MUTATOR MUTANT WITH REDUCED NUCLEOTIDE JRNL TITL 2 DISCRIMINATION AND INCREASED PROTEIN STABILITY JRNL REF BIOCHEMISTRY V. 40 11372 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11560485 JRNL DOI 10.1021/BI010755Y REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1747770.540 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1093 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1283 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1969 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.06000 REMARK 3 B22 (A**2) : -9.59000 REMARK 3 B33 (A**2) : 20.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.28 REMARK 3 BSOL : 20.91 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 1JN3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 22.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL 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) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.6 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 5MM AMMONIUM SULFATE, REMARK 280 150MM SODIUM ACETATE, 50MM HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 298K 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 59.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.81000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.77000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.81000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 493 LIES ON A SPECIAL POSITION. 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 246 REMARK 465 GLU A 247 REMARK 465 ASN A 248 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 ASP A 170 111.22 -174.39 REMARK 500 PRO A 171 -9.41 -59.21 REMARK 500 CYS A 178 -143.81 -103.48 REMARK 500 SER A 204 -97.44 -58.75 REMARK 500 SER A 205 97.56 63.52 REMARK 500 LYS A 206 31.90 143.61 REMARK 500 GLN A 207 61.83 -113.97 REMARK 500 THR A 273 -138.47 -116.61 REMARK 500 SER A 275 153.31 153.57 REMARK 500 LEU A 301 -87.60 -101.20 REMARK 500 THR A 304 -25.36 66.30 REMARK 500 VAL A 306 73.98 31.19 REMARK 500 GLU A 309 95.75 117.86 REMARK 500 GLN A 324 52.71 36.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RPL RELATED DB: PDB DBREF 1JN3 A 85 335 UNP P06766 DPOB_RAT 84 334 SEQADV 1JN3 LEU A 282 UNP P06766 MET 281 ENGINEERED MUTATION 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 LEU 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 *185(H2 O) HELIX 1 1 ASP A 91 THR A 101 1 11 HELIX 2 2 GLY A 107 GLU A 117 1 11 HELIX 3 3 THR A 121 LYS A 127 1 7 HELIX 4 4 ASN A 128 LEU A 132 5 5 HELIX 5 5 ASN A 133 TYR A 142 1 10 HELIX 6 6 GLU A 144 LYS A 148 5 5 HELIX 7 7 ARG A 152 ASP A 170 1 19 HELIX 8 8 CYS A 178 ARG A 183 1 6 HELIX 9 9 GLN A 207 VAL A 221 1 15 HELIX 10 10 PRO A 261 ASP A 263 5 3 HELIX 11 11 GLN A 264 PHE A 272 1 9 HELIX 12 12 SER A 275 LYS A 289 1 15 HELIX 13 13 SER A 315 ILE A 323 1 9 HELIX 14 14 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 N LEU A 194 O THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 254 N MET A 191 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N THR A 225 O VAL A 238 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 N ARG A 299 O THR A 292 CRYST1 119.540 63.620 37.510 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 0.008365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026660 0.00000