PDB Short entry for 2BPF HEADER TRANSFERASE/DNA 19-MAY-94 2BPF TITLE STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TITLE 2 TEMPLATE-PRIMER, AND DDCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3'); COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3'); COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)); COMPND 11 CHAIN: A; COMPND 12 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 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 7 ORGANISM_COMMON: NORWAY RAT; SOURCE 8 ORGANISM_TAXID: 10116; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.PELLETIER,M.R.SAWAYA,A.KUMAR,S.H.WILSON,J.KRAUT REVDAT 3 14-FEB-24 2BPF 1 REMARK LINK REVDAT 2 24-FEB-09 2BPF 1 VERSN REVDAT 1 14-DEC-94 2BPF 0 JRNL AUTH H.PELLETIER,M.R.SAWAYA,A.KUMAR,S.H.WILSON,J.KRAUT JRNL TITL STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, JRNL TITL 2 A DNA TEMPLATE-PRIMER, AND DDCTP. JRNL REF SCIENCE V. 264 1891 1994 JRNL REFN ISSN 0036-8075 JRNL PMID 7516580 REMARK 1 REMARK 1 REFERENCE 1 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: EVIDENCE FOR A REMARK 1 TITL 2 COMMON POLYMERASE MECHANISM REMARK 1 REF SCIENCE V. 264 1930 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 : 13281 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) : 0.193 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 : 2543 REMARK 3 NUCLEIC ACID ATOMS : 305 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 31 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) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 23.560; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.014 ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.005 ; 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 2BPF 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_1000177850. 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 : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR 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 : 13281 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 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: SINGLE WAVELENGTH 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 (%): 65.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.20000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.40000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.80000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 98.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.60000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, 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 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 DC P 7 O3' REMARK 470 PHE A 25 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 28 CG OD1 ND2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 SER A 55 OG REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 LEU A 82 CG CD1 CD2 REMARK 470 GLN A 90 CG CD OE1 NE2 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 220 CG CD CE NZ 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 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 4 O3' DG T 4 C3' -0.147 REMARK 500 DC T 7 O3' DC T 7 C3' -0.060 REMARK 500 DC T 9 N1 DC T 9 C6 -0.047 REMARK 500 DG P 2 O3' DG P 2 C3' -0.051 REMARK 500 DG P 3 O3' DG P 3 C3' -0.047 REMARK 500 DC P 4 O3' DC P 4 C3' -0.050 REMARK 500 DC P 6 N1 DC P 6 C6 -0.057 REMARK 500 DC P 7 N3 DC P 7 C4 -0.043 REMARK 500 GLU A 9 CD GLU A 9 OE1 0.074 REMARK 500 GLU A 21 CD GLU A 21 OE1 0.068 REMARK 500 GLU A 58 CD GLU A 58 OE1 0.075 REMARK 500 GLU A 75 CD GLU A 75 OE1 0.069 REMARK 500 GLU A 86 CD GLU A 86 OE1 0.067 REMARK 500 GLU A 144 CD GLU A 144 OE2 0.071 REMARK 500 GLU A 147 CD GLU A 147 OE1 0.081 REMARK 500 GLU A 153 CD GLU A 153 OE2 0.086 REMARK 500 GLU A 154 CD GLU A 154 OE1 0.082 REMARK 500 GLU A 165 CD GLU A 165 OE1 0.076 REMARK 500 GLU A 172 CD GLU A 172 OE1 0.084 REMARK 500 GLU A 186 CD GLU A 186 OE1 0.069 REMARK 500 GLU A 216 CD GLU A 216 OE1 0.070 REMARK 500 GLU A 232 CD GLU A 232 OE2 0.081 REMARK 500 GLU A 249 CD GLU A 249 OE2 0.071 REMARK 500 GLU A 295 CD GLU A 295 OE2 0.074 REMARK 500 LEU A 301 N LEU A 301 CA -0.132 REMARK 500 GLU A 309 CD GLU A 309 OE1 0.077 REMARK 500 GLU A 329 CD GLU A 329 OE1 0.067 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 DG T 4 C8 - N9 - C1' ANGL. DEV. = 11.3 DEGREES REMARK 500 DG T 4 C4 - N9 - C1' ANGL. DEV. = -11.5 DEGREES REMARK 500 DG T 5 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG T 5 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DG T 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG T 6 C8 - N9 - C1' ANGL. DEV. = 13.1 DEGREES REMARK 500 DG T 6 C4 - N9 - C1' ANGL. DEV. = -12.5 DEGREES REMARK 500 DC T 7 C6 - N1 - C1' ANGL. DEV. = 10.3 DEGREES REMARK 500 DC T 7 C2 - N1 - C1' ANGL. DEV. = -12.2 DEGREES REMARK 500 DG T 8 P - O5' - C5' ANGL. DEV. = -13.7 DEGREES REMARK 500 DG T 8 C8 - N9 - C1' ANGL. DEV. = 28.7 DEGREES REMARK 500 DG T 8 C4 - N9 - C1' ANGL. DEV. = -27.5 DEGREES REMARK 500 DC T 9 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 DC T 9 C6 - N1 - C1' ANGL. DEV. = 13.7 DEGREES REMARK 500 DC T 9 C2 - N1 - C1' ANGL. DEV. = -16.9 DEGREES REMARK 500 DC T 10 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC T 10 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC T 10 C6 - N1 - C2 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC T 10 C6 - N1 - C1' ANGL. DEV. = 7.7 DEGREES REMARK 500 DC T 10 C2 - N1 - C1' ANGL. DEV. = -20.0 DEGREES REMARK 500 DC T 10 C3' - O3' - P ANGL. DEV. = -7.7 DEGREES REMARK 500 DG T 11 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC P 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG P 2 C8 - N9 - C1' ANGL. DEV. = -13.5 DEGREES REMARK 500 DG P 3 P - O5' - C5' ANGL. DEV. = -13.3 DEGREES REMARK 500 DG P 5 P - O5' - C5' ANGL. DEV. = -9.7 DEGREES REMARK 500 DG P 5 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG P 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG P 5 C8 - N9 - C1' ANGL. DEV. = -10.5 DEGREES REMARK 500 DG P 5 C4 - N9 - C1' ANGL. DEV. = 11.0 DEGREES REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC P 6 C6 - N1 - C1' ANGL. DEV. = 9.5 DEGREES REMARK 500 DC P 6 C2 - N1 - C1' ANGL. DEV. = -10.6 DEGREES REMARK 500 DC P 7 O5' - C5' - C4' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC P 7 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DC P 7 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DC P 7 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC P 7 C6 - N1 - C1' ANGL. DEV. = 18.0 DEGREES REMARK 500 DC P 7 C2 - N1 - C1' ANGL. DEV. = -25.4 DEGREES REMARK 500 ASP A 17 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASN A 24 C - N - CA ANGL. DEV. = -16.5 DEGREES REMARK 500 TYR A 39 CB - CG - CD1 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP A 74 CB - CG - OD1 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 92 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 116 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 130 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 145 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 81 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 THR A 10 108.69 -9.48 REMARK 500 LEU A 11 -71.18 -44.33 REMARK 500 THR A 16 -31.58 -38.75 REMARK 500 ASN A 28 -63.17 -94.14 REMARK 500 SER A 30 -154.91 -139.06 REMARK 500 ALA A 32 44.06 -4.87 REMARK 500 LYS A 54 -70.68 -102.30 REMARK 500 THR A 67 -76.89 -17.43 REMARK 500 LYS A 81 171.96 -52.45 REMARK 500 LEU A 82 77.42 179.11 REMARK 500 ILE A 88 -57.18 -21.63 REMARK 500 ARG A 89 4.92 -38.46 REMARK 500 ASP A 91 171.08 5.04 REMARK 500 ASP A 92 -35.22 73.31 REMARK 500 LYS A 120 45.38 -154.80 REMARK 500 ASN A 164 -79.30 -53.76 REMARK 500 ASP A 170 136.73 -174.46 REMARK 500 CYS A 178 -137.10 -95.94 REMARK 500 SER A 202 -1.41 -51.90 REMARK 500 SER A 204 -44.43 153.80 REMARK 500 SER A 205 29.85 35.99 REMARK 500 LYS A 206 -118.62 -110.60 REMARK 500 GLN A 207 57.14 24.91 REMARK 500 LYS A 220 25.08 -63.94 REMARK 500 ARG A 222 60.38 69.93 REMARK 500 PHE A 223 -62.72 -126.00 REMARK 500 THR A 233 -55.30 -137.67 REMARK 500 SER A 243 -171.33 -176.76 REMARK 500 LYS A 262 -29.73 -35.65 REMARK 500 GLU A 295 -9.92 -56.65 REMARK 500 SER A 315 152.64 173.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG T 4 0.08 SIDE CHAIN REMARK 500 DG T 6 0.06 SIDE CHAIN REMARK 500 DC T 9 0.08 SIDE CHAIN REMARK 500 DC T 10 0.18 SIDE CHAIN REMARK 500 DC P 1 0.15 SIDE CHAIN REMARK 500 DG P 2 0.20 SIDE CHAIN REMARK 500 DG P 3 0.12 SIDE CHAIN REMARK 500 DG P 5 0.07 SIDE CHAIN REMARK 500 DC P 7 0.14 SIDE CHAIN 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 MG A 339 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 O REMARK 620 2 ASP A 190 OD1 64.4 REMARK 620 3 ASP A 192 OD2 114.5 67.1 REMARK 620 4 DCT A 338 O2B 171.3 114.1 71.1 REMARK 620 5 DCT A 338 O1A 125.8 63.2 54.2 51.1 REMARK 620 6 DCT A 338 O1G 96.2 79.1 114.9 75.2 61.1 REMARK 620 7 HOH A 419 O 65.7 93.4 76.3 122.9 130.0 161.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 340 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 72.5 REMARK 620 3 DCT A 338 O1A 81.7 91.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A 338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BPG RELATED DB: PDB REMARK 900 2BPF STRUCTURE IS VERY SIMILAR TO THE STRUCTURE IN PDB ENTRY 2BPG REMARK 900 WITH THE FOLLOWING DIFFERENCES: (1) THE STRUCTURE IN THIS ENTRY REMARK 900 CRYSTALLIZED IN SPACE GROUP P 61, WHEREAS THE STRUCTURE IN ENTRY REMARK 900 2BPG CRYSTALLIZED IN SPACE GROUP P 21. (2) THE STRUCTURE IN THIS REMARK 900 ENTRY WAS DETERMINED AT 2.9 ANGSTROMS RESOLUTION, WHEREAS THE REMARK 900 STRUCTURE IN ENTRY 2BPG WAS DETERMINED AT 3.6 ANGSTROMS RESOLUTION. REMARK 900 (3) THE STRUCTURE IN THIS ENTRY HAS ONE MOLECULE IN THE ASYMMETRIC REMARK 900 UNIT, WHEREAS THE STRUCTURE IN ENTRY 2BPG HAS TWO MOLECULES IN THE REMARK 900 ASYMMETRIC UNIT. (4) THE POSITION OF THE 8 KD DOMAIN DIFFERS IN THE REMARK 900 TWO ENTRIES. (5) THE STRUCTURE IN THIS ENTRY INCLUDES TWO REMARK 900 CATALYTICALLY IMPORTANT MG++ IONS, WHEREAS THE STRUCTURE IN ENTRY REMARK 900 2BPG WAS NOT DETERMINED AT A HIGH ENOUGH RESOLUTION TO SEE EVIDENCE REMARK 900 OF THE MG++ IONS IN THE ELECTRON DENSITY MAPS OF THE ACTIVE SITE, REMARK 900 SO THEY ARE NOT INCLUDED IN THAT ENTRY. 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_RAT REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE 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 2BPF A 2 335 UNP P06766 DPOB_RAT 1 334 DBREF 2BPF T 4 11 PDB 2BPF 2BPF 4 11 DBREF 2BPF P 1 7 PDB 2BPF 2BPF 1 7 SEQRES 1 T 8 DG DG DG DC DG DC DC DG SEQRES 1 P 7 DC DG DG DC DG DC DC 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 GLN 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 MG A 339 1 HET MG A 340 1 HET DCT A 338 27 HETNAM MG MAGNESIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 4 MG 2(MG 2+) FORMUL 6 DCT C9 H16 N3 O12 P3 FORMUL 7 HOH *31(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LEU A 62 1 8 HELIX 4 4 GLY A 66 THR A 79 1 14 HELIX 5 5 LEU A 82 ILE A 88 1 7 HELIX 6 6 ARG A 89 ASP A 91 5 3 HELIX 7 7 ASP A 92 ARG A 102 1 11 HELIX 8 8 GLY A 107 GLU A 117 1 11 HELIX 9 9 THR A 121 ASN A 128 1 8 HELIX 10 10 GLU A 129 LEU A 132 5 4 HELIX 11 11 ASN A 133 TYR A 142 1 10 HELIX 12 12 TYR A 142 GLU A 147 1 6 HELIX 13 13 ARG A 152 ASP A 170 1 19 HELIX 14 14 CYS A 178 ARG A 183 1 6 HELIX 15 15 PRO A 208 LYS A 220 1 13 HELIX 16 16 PRO A 261 ASP A 263 5 3 HELIX 17 17 GLN A 264 GLY A 274 1 11 HELIX 18 18 SER A 275 LYS A 289 1 15 HELIX 19 19 SER A 315 ILE A 323 1 9 HELIX 20 20 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 O PHE A 235 N 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 O ARG A 299 N THR A 292 LINK O ASP A 190 MG MG A 339 1555 1555 3.09 LINK OD1 ASP A 190 MG MG A 339 1555 1555 2.08 LINK OD2 ASP A 190 MG MG A 340 1555 1555 2.03 LINK OD2 ASP A 192 MG MG A 339 1555 1555 2.54 LINK OD1 ASP A 192 MG MG A 340 1555 1555 2.46 LINK O2B DCT A 338 MG MG A 339 1555 1555 1.72 LINK O1A DCT A 338 MG MG A 339 1555 1555 2.95 LINK O1G DCT A 338 MG MG A 339 1555 1555 2.27 LINK O1A DCT A 338 MG MG A 340 1555 1555 2.63 LINK MG MG A 339 O HOH A 419 1555 1555 2.54 CISPEP 1 GLY A 274 SER A 275 0 -0.37 SITE 1 AC1 6 SER A 180 SER A 188 ASP A 190 ASP A 192 SITE 2 AC1 6 DCT A 338 HOH A 419 SITE 1 AC2 4 ASP A 190 ASP A 192 ASP A 256 DCT A 338 SITE 1 AC3 17 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC3 17 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC3 17 PHE A 272 GLY A 274 ASP A 276 ASN A 279 SITE 4 AC3 17 MG A 339 MG A 340 HOH A 408 DC P 7 SITE 5 AC3 17 DG T 4 CRYST1 94.900 94.900 117.600 90.00 90.00 120.00 P 61 6 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 0.010537 0.006084 0.000000 0.00000 SCALE2 0.000000 0.012168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008503 0.00000