HEADER NUCLEOTIDYLTRANSFERASE 12-APR-94 1BPE TITLE CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON TITLE 2 POLYMERASE MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116 KEYWDS NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT REVDAT 5 07-FEB-24 1BPE 1 REMARK SEQADV REVDAT 4 24-FEB-09 1BPE 1 VERSN REVDAT 3 01-APR-03 1BPE 1 JRNL REVDAT 2 15-OCT-94 1BPE 1 SOURCE REMARK REVDAT 1 31-JUL-94 1BPE 0 JRNL AUTH M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT JRNL TITL CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A JRNL TITL 2 COMMON POLYMERASE MECHANISM. JRNL REF SCIENCE V. 264 1930 1994 JRNL REFN ISSN 0036-8075 JRNL PMID 7516581 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,S.H.WILSON,J.KRAUT REMARK 1 TITL STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, REMARK 1 TITL 2 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4069 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) : 0.199 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) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2128 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 0 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) : 0.019 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 3.000 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BPE 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_1000171980. 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 <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) : 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 34.10400 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: 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 THR A 10 REMARK 465 LEU A 11 REMARK 465 GLU A 26 REMARK 465 LYS A 27 REMARK 465 ASN A 28 REMARK 465 VAL A 29 REMARK 465 SER A 30 REMARK 465 GLN A 31 REMARK 465 ALA A 32 REMARK 465 ILE A 33 REMARK 465 HIS A 34 REMARK 465 LYS A 35 REMARK 465 TYR A 36 REMARK 465 ASN A 37 REMARK 465 ALA A 38 REMARK 465 TYR A 39 REMARK 465 ARG A 40 REMARK 465 LYS A 41 REMARK 465 ALA A 42 REMARK 465 ALA A 43 REMARK 465 SER A 44 REMARK 465 VAL A 45 REMARK 465 ILE A 46 REMARK 465 ALA A 47 REMARK 465 LYS A 48 REMARK 465 TYR A 49 REMARK 465 PRO A 50 REMARK 465 HIS A 51 REMARK 465 LYS A 52 REMARK 465 ILE A 53 REMARK 465 LYS A 54 REMARK 465 SER A 55 REMARK 465 GLY A 64 REMARK 465 VAL A 65 REMARK 465 GLY A 66 REMARK 465 THR A 67 REMARK 465 LYS A 68 REMARK 465 ILE A 69 REMARK 465 ALA A 70 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 ASN A 248 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 12 CG OD1 ND2 REMARK 470 ILE A 15 CG1 CG2 CD1 REMARK 470 THR A 16 OG1 CG2 REMARK 470 ASP A 17 CG OD1 OD2 REMARK 470 MET A 18 CG SD CE REMARK 470 LEU A 19 CG CD1 CD2 REMARK 470 VAL A 20 CG1 CG2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LEU A 22 CG CD1 CD2 REMARK 470 ASN A 24 CG OD1 ND2 REMARK 470 PHE A 25 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LEU A 62 CG CD1 CD2 REMARK 470 PRO A 63 CG CD REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 ILE A 73 CG1 CG2 CD1 REMARK 470 ASP A 74 CG OD1 OD2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 LEU A 77 CG CD1 CD2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 LEU A 82 CG CD1 CD2 REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 LEU A 85 CG CD1 CD2 REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 ILE A 88 CG1 CG2 CD1 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 ASP A 92 CG OD1 OD2 REMARK 470 SER A 109 OG REMARK 470 ILE A 119 CG1 CG2 CD1 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 159 CG CD OE1 NE2 REMARK 470 SER A 243 OG REMARK 470 GLU A 244 CG CD OE1 OE2 REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 ILE A 293 CG1 CG2 CD1 REMARK 470 VAL A 303 CG1 CG2 REMARK 470 THR A 304 OG1 CG2 REMARK 470 VAL A 306 CG1 CG2 REMARK 470 ARG A 326 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N THR A 227 OE2 GLU A 335 2656 2.06 REMARK 500 CA ASP A 226 OE2 GLU A 335 2656 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 74 N ASP A 74 CA 0.160 REMARK 500 GLU A 117 CD GLU A 117 OE1 0.068 REMARK 500 GLU A 144 CD GLU A 144 OE1 0.070 REMARK 500 GLU A 147 CD GLU A 147 OE1 0.075 REMARK 500 GLU A 153 CD GLU A 153 OE2 0.072 REMARK 500 GLU A 165 CD GLU A 165 OE1 0.071 REMARK 500 GLU A 172 CD GLU A 172 OE2 0.068 REMARK 500 GLU A 186 CD GLU A 186 OE1 0.067 REMARK 500 GLU A 203 CD GLU A 203 OE1 0.071 REMARK 500 GLU A 232 CD GLU A 232 OE1 0.069 REMARK 500 GLU A 249 CD GLU A 249 OE1 0.072 REMARK 500 GLU A 288 CD GLU A 288 OE1 0.081 REMARK 500 GLU A 295 CD GLU A 295 OE1 0.070 REMARK 500 GLU A 329 CD GLU A 329 OE1 0.071 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 PRO A 63 N - CA - CB ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 74 C - N - CA ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP A 74 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP A 74 N - CA - C ANGL. DEV. = 18.1 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 130 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 145 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 PRO A 151 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO A 151 C - N - CD ANGL. DEV. = -36.1 DEGREES REMARK 500 ASP A 160 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 PRO A 171 C - N - CD ANGL. DEV. = -32.7 DEGREES REMARK 500 ASP A 192 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 222 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 PRO A 242 C - N - CD ANGL. DEV. = -33.3 DEGREES REMARK 500 PRO A 251 C - N - CD ANGL. DEV. = -16.0 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 256 CB - CG - OD1 ANGL. DEV. = -8.7 DEGREES REMARK 500 SER A 275 CB - CA - C ANGL. DEV. = -13.8 DEGREES REMARK 500 ASP A 276 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 299 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 318 CB - CG - OD1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 318 CB - CG - OD2 ANGL. DEV. = 5.7 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 73 176.74 179.84 REMARK 500 ASP A 74 14.76 -50.45 REMARK 500 THR A 79 134.10 111.77 REMARK 500 LYS A 81 -139.46 95.80 REMARK 500 GLU A 86 8.82 42.87 REMARK 500 ALA A 110 -82.04 -33.87 REMARK 500 GLU A 117 49.07 -74.59 REMARK 500 LYS A 120 -31.20 -173.53 REMARK 500 ASN A 128 31.71 -53.61 REMARK 500 ASP A 130 -38.77 -29.12 REMARK 500 LYS A 131 0.25 -67.76 REMARK 500 HIS A 135 -96.80 -56.75 REMARK 500 GLN A 136 -25.77 -36.99 REMARK 500 PHE A 143 -47.80 8.48 REMARK 500 ARG A 152 1.70 -56.70 REMARK 500 ASP A 160 -80.91 -59.91 REMARK 500 ILE A 161 -33.56 -35.55 REMARK 500 CYS A 178 -138.77 -128.84 REMARK 500 PHE A 181 -34.33 -39.19 REMARK 500 ARG A 183 -13.62 -48.25 REMARK 500 ALA A 185 145.44 -24.14 REMARK 500 SER A 188 -142.79 -92.17 REMARK 500 ASP A 192 91.52 -168.06 REMARK 500 LYS A 206 80.87 -170.31 REMARK 500 GLN A 207 36.62 -157.55 REMARK 500 LEU A 210 -70.57 -51.96 REMARK 500 GLN A 217 -71.93 -48.40 REMARK 500 LEU A 218 -18.76 -40.66 REMARK 500 VAL A 221 0.04 -64.61 REMARK 500 LEU A 228 -81.68 -71.53 REMARK 500 SER A 229 -160.24 -114.82 REMARK 500 LYS A 230 135.51 177.95 REMARK 500 GLU A 232 -63.44 55.41 REMARK 500 CYS A 239 -159.22 -97.18 REMARK 500 GLN A 240 118.81 164.50 REMARK 500 SER A 243 -169.27 -111.02 REMARK 500 GLU A 244 13.45 167.63 REMARK 500 TYR A 265 -73.37 -39.27 REMARK 500 SER A 275 -167.36 -73.39 REMARK 500 ASP A 276 -76.54 -54.98 REMARK 500 ALA A 284 -79.95 -56.82 REMARK 500 LEU A 301 -142.96 -67.47 REMARK 500 THR A 304 4.74 111.49 REMARK 500 ALA A 307 166.56 177.16 REMARK 500 GLU A 309 120.88 146.47 REMARK 500 ASP A 314 -72.45 -64.10 REMARK 500 GLN A 317 -15.07 -46.17 REMARK 500 GLN A 324 106.76 36.32 REMARK 500 TYR A 327 81.71 -57.43 REMARK 500 ARG A 328 82.76 -67.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 73 ASP A 74 121.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A 338 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: DPOB_HUMAN REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 GLN 89 ARG 90 REMARK 999 ARG 227 LEU 228 REMARK 999 REMARK 999 THE N-TERMINAL METHIONINE IS INCLUDED IN THE GENE SEQUENCE REMARK 999 EVEN THOUGH IT IS REMOVED AFTER TRANSLATION IN THE CELL; REMARK 999 SEE MATSUKAGE ET AL., J. BIOL. CHEM. 262, 8960, (1987). REMARK 999 FOR THE AMINO ACID SEQUENCE SEE A. KUMAR ET AL., J. BIOL. REMARK 999 CHEM. 265, 2124, (1990). DBREF 1BPE A 2 335 UNP P06766 DPOB_RAT 1 334 SEQADV 1BPE ARG A 90 UNP P06766 GLN 89 CONFLICT 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 VAL 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 ARG ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL THR SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS LEU 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 GLU 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 LEU SEQRES 14 A 335 ASP PRO 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 ASN PHE THR SER GLU SER SER LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS ARG VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 ARG 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 GLU ASN ASP GLU SEQRES 20 A 335 ASN 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 GLN ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 ARG TYR ARG GLU PRO LYS ASP ARG SER GLU HET DTP A 338 30 HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE FORMUL 2 DTP C10 H16 N5 O12 P3 HELIX 1 1 ASN A 12 PHE A 25 1 14 HELIX 2 2 ASP A 74 THR A 79 1 6 HELIX 3 3 LYS A 81 GLU A 86 1 6 HELIX 4 4 THR A 93 ARG A 102 1 10 HELIX 5 5 GLY A 107 GLU A 117 1 11 HELIX 6 6 THR A 121 ASN A 128 1 8 HELIX 7 7 GLU A 129 LEU A 132 5 4 HELIX 8 8 ASN A 133 TYR A 142 1 10 HELIX 9 9 GLU A 144 LYS A 148 5 5 HELIX 10 10 PRO A 151 ASP A 170 1 20 HELIX 11 11 CYS A 178 GLY A 184 1 7 HELIX 12 12 PRO A 208 VAL A 221 1 14 HELIX 13 13 GLN A 264 GLY A 274 1 11 HELIX 14 14 ILE A 277 LYS A 289 1 13 HELIX 15 15 GLU A 316 ILE A 323 1 8 HELIX 16 16 GLU A 329 ARG A 333 5 5 SHEET 1 A 5 ILE A 174 VAL A 177 0 SHEET 2 A 5 VAL A 193 THR A 196 -1 N LEU A 194 O THR A 176 SHEET 3 A 5 ARG A 254 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 A 5 LYS A 234 VAL A 238 -1 N PHE A 235 O ILE A 257 SHEET 5 A 5 ASP A 226 THR A 227 -1 N ASP A 226 O VAL A 238 SHEET 1 B 2 PHE A 291 THR A 292 0 SHEET 2 B 2 ARG A 299 PRO A 300 -1 N ARG A 299 O THR A 292 CISPEP 1 GLY A 274 SER A 275 0 0.24 SITE 1 AC1 4 SER A 180 SER A 188 GLY A 189 ASP A 190 CRYST1 39.319 68.208 75.038 90.00 91.77 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 0.025433 0.000000 0.000786 0.00000 SCALE2 0.000000 0.014661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013333 0.00000