HEADER TRANSFERASE/DNA 05-DEC-07 3BJY TITLE CATALYTIC CORE OF REV1 IN COMPLEX WITH DNA (MODIFIED TEMPLATE GUANINE) TITLE 2 AND INCOMING NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN REV1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*DTP*DAP*DAP*(P) COMPND 9 P*DGP*DTP*DAP*DGP*DGP*DGP*DGP*DAP*DGP*DGP*DAP*DT)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*DAP*DTP*DCP*DCP*DTP*DCP*DCP*DCP*DCP*DTP*DAP*(DOC))-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: REV1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_COMMON: YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BJ5464; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBJ954; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES KEYWDS DNA POLYMERASE, PROTEIN-DNA COMPLEX, ADDUCT, BYPASS, DNA DAMAGE, DNA KEYWDS 2 REPAIR, DNA SYNTHESIS, DNA-BINDING, MAGNESIUM, METAL-BINDING, KEYWDS 3 NUCLEOTIDYLTRANSFERASE, NUCLEUS, TRANSFERASE, TRANSFERASE-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.T.NAIR,R.E.JOHNSON,L.PRAKASH,S.PRAKASH,A.K.AGGARWAL REVDAT 3 01-NOV-23 3BJY 1 REMARK SEQRES REVDAT 2 24-FEB-09 3BJY 1 VERSN REVDAT 1 28-OCT-08 3BJY 0 JRNL AUTH D.T.NAIR,R.E.JOHNSON,L.PRAKASH,S.PRAKASH,A.K.AGGARWAL JRNL TITL PROTEIN-TEMPLATE-DIRECTED SYNTHESIS ACROSS AN JRNL TITL 2 ACROLEIN-DERIVED DNA ADDUCT BY YEAST REV1 DNA POLYMERASE JRNL REF STRUCTURE V. 16 239 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18275815 JRNL DOI 10.1016/J.STR.2007.12.009 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38556 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3862 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 : 3370 REMARK 3 NUCLEIC ACID ATOMS : 572 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 158 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3BJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.410 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.16400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2AQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 5K MME, 0.4M AMMONOIUM REMARK 280 SULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.83850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.83850 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 90.53100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 99.78900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 90.53100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 99.78900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.83850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 90.53100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 99.78900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.83850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 90.53100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 99.78900 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 ASN A 478 REMARK 465 ILE A 479 REMARK 465 HIS A 480 REMARK 465 ASN A 481 REMARK 465 THR A 482 REMARK 465 ASN A 483 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 LYS A 305 CG CD CE NZ REMARK 470 TYR A 347 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 353 CG CD CE NZ REMARK 470 ARG A 386 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 GLU A 439 CG CD OE1 OE2 REMARK 470 LYS A 453 CG CD CE NZ REMARK 470 GLU A 540 CG CD OE1 OE2 REMARK 470 GLU A 616 CG CD OE1 OE2 REMARK 470 LYS A 653 CG CD CE NZ REMARK 470 LYS A 673 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN A 459 O HOH A 809 2.03 REMARK 500 OP2 DOC P 12 O HOH P 144 2.11 REMARK 500 OE1 GLN A 495 NE2 GLN A 499 2.14 REMARK 500 O CYS A 510 O ILE A 531 2.19 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 PHE A 367 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 PHE A 367 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 LEU A 460 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 PRO A 526 CA - N - CD ANGL. DEV. = -8.5 DEGREES REMARK 500 PRO A 679 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 PRO A 679 C - N - CD ANGL. DEV. = -14.8 DEGREES REMARK 500 DG T 5 N9 - C1' - C2' ANGL. DEV. = 9.6 DEGREES REMARK 500 DT T 6 C5' - C4' - C3' ANGL. DEV. = -16.0 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG T 8 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG T 8 N9 - C1' - C2' ANGL. DEV. = 11.9 DEGREES REMARK 500 DG T 8 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG T 9 C4 - N9 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 DG T 10 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG T 11 N9 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 DG T 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG T 13 N9 - C1' - C2' ANGL. DEV. = 10.3 DEGREES REMARK 500 DG T 13 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG T 14 N9 - C1' - C2' ANGL. DEV. = 10.9 DEGREES REMARK 500 DG T 14 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA T 15 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC P 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC P 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 2.1 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 ARG A 306 104.72 71.82 REMARK 500 CYS A 365 65.37 24.69 REMARK 500 LYS A 396 -88.41 -127.60 REMARK 500 ASN A 397 50.52 -96.52 REMARK 500 ASN A 456 68.55 -113.18 REMARK 500 ASN A 502 -136.91 81.33 REMARK 500 LYS A 525 -65.64 -15.70 REMARK 500 PRO A 526 85.04 -58.03 REMARK 500 ILE A 531 -72.85 -93.08 REMARK 500 THR A 532 93.35 52.53 REMARK 500 SER A 567 72.30 37.40 REMARK 500 ASP A 613 86.76 -172.85 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 DA T 3 0.08 SIDE CHAIN REMARK 500 DG T 5 0.09 SIDE CHAIN REMARK 500 DG T 10 0.05 SIDE CHAIN 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 DCP A 739 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 298 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AQ4 RELATED DB: PDB REMARK 900 CATALYTIC CORE OF REV1 IN COMPLEX WITH DNA AND INCOMING NULCEOTIDE DBREF 3BJY A 305 738 UNP P12689 REV1_YEAST 305 738 DBREF 3BJY T 1 16 PDB 3BJY 3BJY 1 16 DBREF 3BJY P 1 12 PDB 3BJY 3BJY 1 12 SEQRES 1 A 434 LYS ARG ILE VAL ALA CYS ASP ASP PRO ASP PHE LEU THR SEQRES 2 A 434 SER TYR PHE ALA HIS SER ARG LEU HIS HIS LEU SER ALA SEQRES 3 A 434 TRP LYS ALA ASN LEU LYS ASP LYS PHE LEU ASN GLU ASN SEQRES 4 A 434 ILE HIS LYS TYR THR LYS ILE THR ASP LYS ASP THR TYR SEQRES 5 A 434 ILE ILE PHE HIS ILE ASP PHE ASP CYS PHE PHE ALA THR SEQRES 6 A 434 VAL ALA TYR LEU CYS ARG SER SER SER PHE SER ALA CYS SEQRES 7 A 434 ASP PHE LYS ARG ASP PRO ILE VAL VAL CYS HIS GLY THR SEQRES 8 A 434 LYS ASN SER ASP ILE ALA SER CYS ASN TYR VAL ALA ARG SEQRES 9 A 434 SER TYR GLY ILE LYS ASN GLY MET TRP VAL SER GLN ALA SEQRES 10 A 434 GLU LYS MET LEU PRO ASN GLY ILE LYS LEU ILE SER LEU SEQRES 11 A 434 PRO TYR THR PHE GLU GLN PHE GLN LEU LYS SER GLU ALA SEQRES 12 A 434 PHE TYR SER THR LEU LYS ARG LEU ASN ILE PHE ASN LEU SEQRES 13 A 434 ILE LEU PRO ILE SER ILE ASP GLU ALA VAL CYS VAL ARG SEQRES 14 A 434 ILE ILE PRO ASP ASN ILE HIS ASN THR ASN THR LEU ASN SEQRES 15 A 434 ALA ARG LEU CYS GLU GLU ILE ARG GLN GLU ILE PHE GLN SEQRES 16 A 434 GLY THR ASN GLY CYS THR VAL SER ILE GLY CYS SER ASP SEQRES 17 A 434 SER LEU VAL LEU ALA ARG LEU ALA LEU LYS MET ALA LYS SEQRES 18 A 434 PRO ASN GLY TYR ASN ILE THR PHE LYS SER ASN LEU SER SEQRES 19 A 434 GLU GLU PHE TRP SER SER PHE LYS LEU ASP ASP LEU PRO SEQRES 20 A 434 GLY VAL GLY HIS SER THR LEU SER ARG LEU GLU SER THR SEQRES 21 A 434 PHE ASP SER PRO HIS SER LEU ASN ASP LEU ARG LYS ARG SEQRES 22 A 434 TYR THR LEU ASP ALA LEU LYS ALA SER VAL GLY SER LYS SEQRES 23 A 434 LEU GLY MET LYS ILE HIS LEU ALA LEU GLN GLY GLN ASP SEQRES 24 A 434 ASP GLU GLU SER LEU LYS ILE LEU TYR ASP PRO LYS GLU SEQRES 25 A 434 VAL LEU GLN ARG LYS SER LEU SER ILE ASP ILE ASN TRP SEQRES 26 A 434 GLY ILE ARG PHE LYS ASN ILE THR GLN VAL ASP LEU PHE SEQRES 27 A 434 ILE GLU ARG GLY CYS GLN TYR LEU LEU GLU LYS LEU ASN SEQRES 28 A 434 GLU ILE ASN LYS THR THR SER GLN ILE THR LEU LYS LEU SEQRES 29 A 434 MET ARG ARG CYS LYS ASP ALA PRO ILE GLU PRO PRO LYS SEQRES 30 A 434 TYR MET GLY MET GLY ARG CYS ASP SER PHE SER ARG SER SEQRES 31 A 434 SER ARG LEU GLY ILE PRO THR ASN GLU PHE GLY ILE ILE SEQRES 32 A 434 ALA THR GLU MET LYS SER LEU TYR ARG THR LEU GLY CYS SEQRES 33 A 434 PRO PRO MET GLU LEU ARG GLY LEU ALA LEU GLN PHE ASN SEQRES 34 A 434 LYS LEU VAL ASP VAL SEQRES 1 T 16 DT DA DA P DG DT DA DG DG DG DG DA DG SEQRES 2 T 16 DG DA DT SEQRES 1 P 12 DA DT DC DC DT DC DC DC DC DT DA DOC MODRES 3BJY P T 4 DG MODRES 3BJY DOC P 12 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET P T 4 25 HET DOC P 12 18 HET DCP A 739 28 HET MG A 297 1 HET MG A 298 1 HETNAM P 2'-DEOXY-N1,N2-PROPANO GUANOSINE MONOPHOSPHATE HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 P C13 H18 N5 O7 P FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 4 DCP C9 H16 N3 O13 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *158(H2 O) HELIX 1 1 ASP A 314 SER A 323 1 10 HELIX 2 2 SER A 323 ASN A 343 1 21 HELIX 3 3 CYS A 365 CYS A 374 1 10 HELIX 4 4 SER A 376 SER A 380 5 5 HELIX 5 5 ASN A 404 TYR A 410 1 7 HELIX 6 6 TRP A 417 MET A 424 1 8 HELIX 7 7 THR A 437 LEU A 455 1 19 HELIX 8 8 THR A 484 ASN A 502 1 19 HELIX 9 9 SER A 513 LYS A 525 1 13 HELIX 10 10 PHE A 533 LEU A 537 5 5 HELIX 11 11 SER A 538 SER A 543 1 6 HELIX 12 12 LYS A 546 LEU A 550 5 5 HELIX 13 13 GLY A 554 PHE A 565 1 12 HELIX 14 14 SER A 570 TYR A 578 1 9 HELIX 15 15 THR A 579 GLY A 588 1 10 HELIX 16 16 GLY A 588 LEU A 599 1 12 HELIX 17 17 ASP A 604 ASP A 613 1 10 HELIX 18 18 ASP A 613 LEU A 618 1 6 HELIX 19 19 ASN A 635 ILE A 657 1 23 HELIX 20 20 GLU A 703 GLY A 719 1 17 HELIX 21 21 PRO A 721 MET A 723 5 3 SHEET 1 A 5 LEU A 460 SER A 465 0 SHEET 2 A 5 GLU A 468 ILE A 474 -1 O VAL A 472 N LEU A 460 SHEET 3 A 5 TYR A 356 PHE A 363 -1 N ILE A 361 O ALA A 469 SHEET 4 A 5 VAL A 506 SER A 511 -1 O SER A 511 N ILE A 358 SHEET 5 A 5 TYR A 529 ASN A 530 1 O ASN A 530 N CYS A 510 SHEET 1 B 3 SER A 402 CYS A 403 0 SHEET 2 B 3 ILE A 389 VAL A 391 -1 N VAL A 391 O SER A 402 SHEET 3 B 3 ILE A 432 LEU A 434 1 O LEU A 434 N VAL A 390 SHEET 1 C 4 LEU A 623 ILE A 627 0 SHEET 2 C 4 LEU A 725 ASP A 737 -1 O PHE A 732 N LEU A 623 SHEET 3 C 4 LYS A 659 ARG A 671 -1 N LYS A 667 O ALA A 729 SHEET 4 C 4 CYS A 688 THR A 701 -1 O LEU A 697 N SER A 662 SITE 1 AC1 21 MG A 297 MG A 298 ARG A 324 LEU A 328 SITE 2 AC1 21 ASP A 362 PHE A 363 ASP A 364 CYS A 365 SITE 3 AC1 21 PHE A 366 PHE A 367 ALA A 401 SER A 402 SITE 4 AC1 21 TYR A 405 ARG A 408 ASN A 414 ASP A 467 SITE 5 AC1 21 LYS A 525 HOH A 748 HOH A 753 HOH A 791 SITE 6 AC1 21 HOH A 850 SITE 1 AC2 6 MG A 298 ASP A 362 ASP A 467 GLU A 468 SITE 2 AC2 6 DCP A 739 DOC P 12 SITE 1 AC3 5 MG A 297 ASP A 362 PHE A 363 ASP A 467 SITE 2 AC3 5 DCP A 739 CRYST1 181.062 199.578 55.677 90.00 90.00 90.00 C 2 2 21 8 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 0.005523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017961 0.00000