PDB Short entry for 2KZM HEADER TRANSFERASE/DNA 03-JUL-98 2KZM TITLE KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*TP*A*CP*GP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RANDOM SEQUENCE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN (DNA POLYMERASE I); COMPND 8 CHAIN: A; COMPND 9 FRAGMENT: KLENOW FRAGMENT, LARGE FRAGMENT; COMPND 10 SYNONYM: POL I; COMPND 11 EC: 2.7.7.7; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CJ376; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCJ155 KEYWDS POLYMERASE, EXONUCLEASE, TWO METAL ION, NUCLEOTIDYLTRANSFERASE-DNA KEYWDS 2 COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.BRAUTIGAM,S.SUN,J.A.PICCIRILLI,T.A.STEITZ REVDAT 3 03-NOV-21 2KZM 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2KZM 1 VERSN REVDAT 1 16-FEB-99 2KZM 0 JRNL AUTH C.A.BRAUTIGAM,S.SUN,J.A.PICCIRILLI,T.A.STEITZ JRNL TITL STRUCTURES OF NORMAL SINGLE-STRANDED DNA AND JRNL TITL 2 DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES BOUND TO THE 3'-5' JRNL TITL 3 EXONUCLEOLYTIC ACTIVE SITE OF DNA POLYMERASE I FROM JRNL TITL 4 ESCHERICHIA COLI. JRNL REF BIOCHEMISTRY V. 38 696 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 9888810 JRNL DOI 10.1021/BI981537G REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.BRAUTIGAM,T.A.STEITZ REMARK 1 TITL STRUCTURAL PRINCIPLES FOR THE INHIBITION OF THE 3'-5' REMARK 1 TITL 2 EXONUCLEASE ACTIVITY OF ESCHERICHIA COLI DNA POLYMERASE I BY REMARK 1 TITL 3 PHOSPHOROTHIOATES REMARK 1 REF J.MOL.BIOL. V. 277 363 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 22445 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) : 0.195 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1815 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 : 30 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 438 REMARK 3 BIN R VALUE (WORKING SET) : 0.2683 REMARK 3 BIN FREE R VALUE : 0.2716 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 44 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 : 4753 REMARK 3 NUCLEIC ACID ATOMS : 42 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 98 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) : 0.30 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : CHAD_PARAM.DNA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : CHAD_TOP.DNA REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 BULK-SOLVENT CORRECTION WAS USED TO EXTEND LOW-RES LIMIT TO 20 REMARK 3 ANGSTROMS. REMARK 3 REMARK 3 ONLY THE LAST TWO NUCLEOTIDES OF NUCLEIC ACID COULD BE REMARK 3 MODELED INTO THE ELECTRON DENSITY. REMARK 4 REMARK 4 2KZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000178289. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID-BODY REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: STRUCTURE WAS SOLVED USING IN-HOUSE HIGH-RESOLUTION REMARK 200 STRUCTURE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM CITRATE PH 5.8, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 43.10000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.65000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.55000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 DG B 1001 REMARK 465 DC B 1002 REMARK 465 DT B 1003 REMARK 465 DT B 1004 REMARK 465 DA B 1005 REMARK 465 PRO A 603 REMARK 465 GLY A 604 REMARK 465 GLY A 605 REMARK 465 ALA A 606 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 B1006 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DC B1006 C3' C2' C1' N1 C2 O2 N3 REMARK 470 DC B1006 C4 N4 C5 C6 REMARK 470 LEU A 599 CG CD1 CD2 REMARK 470 LYS A 600 CG CD CE NZ REMARK 470 LYS A 601 CG CD CE NZ REMARK 470 THR A 602 OG1 CG2 REMARK 470 PRO A 607 CG CD REMARK 470 SER A 608 OG REMARK 470 THR A 609 OG1 CG2 REMARK 470 SER A 610 OG REMARK 470 GLU A 611 CG CD OE1 OE2 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 DC B1006 O3' DG B1007 P -0.380 REMARK 500 DG B1007 P DG B1007 O5' 0.096 REMARK 500 DG B1007 C5' DG B1007 C4' 0.046 REMARK 500 DG B1007 C2' DG B1007 C1' 0.282 REMARK 500 DG B1007 O4' DG B1007 C1' -0.118 REMARK 500 DG B1007 N1 DG B1007 C2 0.072 REMARK 500 DG B1007 C5 DG B1007 C6 -0.093 REMARK 500 DG B1007 C5 DG B1007 N7 -0.061 REMARK 500 DG B1007 N9 DG B1007 C4 -0.065 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 B1007 O3' - P - O5' ANGL. DEV. = -22.9 DEGREES REMARK 500 DG B1007 O3' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DG B1007 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES REMARK 500 DG B1007 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES REMARK 500 DG B1007 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B1007 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG B1007 O4' - C1' - N9 ANGL. DEV. = 11.3 DEGREES REMARK 500 DG B1007 C2 - N3 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B1007 N3 - C4 - C5 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B1007 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B1007 C5 - C6 - N1 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B1007 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B1007 C6 - C5 - N7 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG B1007 N1 - C6 - O6 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B1007 C8 - N9 - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 DG B1007 C4 - N9 - C1' ANGL. DEV. = -8.2 DEGREES REMARK 500 DG B1007 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 DC B1008 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B1008 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B1008 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B1008 N1 - C2 - N3 ANGL. DEV. = 6.5 DEGREES REMARK 500 DC B1008 N3 - C2 - O2 ANGL. DEV. = -8.0 DEGREES REMARK 500 LYS A 597 N - CA - C ANGL. DEV. = 19.6 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 SER A 326 -168.44 -107.06 REMARK 500 GLU A 376 149.82 -173.74 REMARK 500 ASN A 420 60.78 64.43 REMARK 500 ASN A 450 101.85 -170.61 REMARK 500 ASN A 482 30.45 -84.43 REMARK 500 LEU A 516 -7.33 -59.87 REMARK 500 ILE A 529 -66.95 -104.73 REMARK 500 ALA A 574 -122.29 -108.45 REMARK 500 GLU A 576 -176.72 44.81 REMARK 500 LEU A 580 34.91 -99.08 REMARK 500 THR A 583 24.03 49.43 REMARK 500 LYS A 584 -68.34 -145.89 REMARK 500 GLN A 594 131.64 87.85 REMARK 500 LYS A 597 -55.60 2.43 REMARK 500 LEU A 599 -163.89 -103.82 REMARK 500 THR A 609 36.64 -88.76 REMARK 500 SER A 610 -36.82 -143.33 REMARK 500 ASP A 620 -35.80 -144.30 REMARK 500 ALA A 662 61.12 -116.79 REMARK 500 ASP A 673 64.94 33.16 REMARK 500 VAL A 681 -62.69 -93.00 REMARK 500 ASN A 683 141.41 -175.52 REMARK 500 GLN A 708 60.83 32.92 REMARK 500 LYS A 782 -7.90 61.87 REMARK 500 ALA A 807 -71.72 -70.26 REMARK 500 SER A 830 -32.69 -33.70 REMARK 500 SER A 831 -6.66 73.95 REMARK 500 HIS A 881 -117.53 56.25 REMARK 500 THR A 908 -131.07 -126.21 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 MN B 2 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B1007 O3' REMARK 620 2 DC B1008 OP1 56.8 REMARK 620 3 ASP A 355 OD1 153.4 96.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B1008 OP1 REMARK 620 2 ASP A 355 OD2 108.4 REMARK 620 3 GLU A 357 OE2 115.3 91.0 REMARK 620 4 ASP A 501 OD2 105.9 108.1 125.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: EXO REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: EXONUCLEASE ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 2 DBREF 2KZM A 324 928 UNP P00582 DPO1_ECOLI 324 928 DBREF 2KZM B 1001 1008 PDB 2KZM 2KZM 1001 1008 SEQADV 2KZM MET A 324 UNP P00582 VAL 324 ENGINEERED MUTATION SEQRES 1 B 8 DG DC DT DT DA DC DG DC SEQRES 1 A 605 MET ILE SER TYR ASP ASN TYR VAL THR ILE LEU ASP GLU SEQRES 2 A 605 GLU THR LEU LYS ALA TRP ILE ALA LYS LEU GLU LYS ALA SEQRES 3 A 605 PRO VAL PHE ALA PHE ASP THR GLU THR ASP SER LEU ASP SEQRES 4 A 605 ASN ILE SER ALA ASN LEU VAL GLY LEU SER PHE ALA ILE SEQRES 5 A 605 GLU PRO GLY VAL ALA ALA TYR ILE PRO VAL ALA HIS ASP SEQRES 6 A 605 TYR LEU ASP ALA PRO ASP GLN ILE SER ARG GLU ARG ALA SEQRES 7 A 605 LEU GLU LEU LEU LYS PRO LEU LEU GLU ASP GLU LYS ALA SEQRES 8 A 605 LEU LYS VAL GLY GLN ASN LEU LYS TYR ASP ARG GLY ILE SEQRES 9 A 605 LEU ALA ASN TYR GLY ILE GLU LEU ARG GLY ILE ALA PHE SEQRES 10 A 605 ASP THR MET LEU GLU SER TYR ILE LEU ASN SER VAL ALA SEQRES 11 A 605 GLY ARG HIS ASP MET ASP SER LEU ALA GLU ARG TRP LEU SEQRES 12 A 605 LYS HIS LYS THR ILE THR PHE GLU GLU ILE ALA GLY LYS SEQRES 13 A 605 GLY LYS ASN GLN LEU THR PHE ASN GLN ILE ALA LEU GLU SEQRES 14 A 605 GLU ALA GLY ARG TYR ALA ALA GLU ASP ALA ASP VAL THR SEQRES 15 A 605 LEU GLN LEU HIS LEU LYS MET TRP PRO ASP LEU GLN LYS SEQRES 16 A 605 HIS LYS GLY PRO LEU ASN VAL PHE GLU ASN ILE GLU MET SEQRES 17 A 605 PRO LEU VAL PRO VAL LEU SER ARG ILE GLU ARG ASN GLY SEQRES 18 A 605 VAL LYS ILE ASP PRO LYS VAL LEU HIS ASN HIS SER GLU SEQRES 19 A 605 GLU LEU THR LEU ARG LEU ALA GLU LEU GLU LYS LYS ALA SEQRES 20 A 605 HIS GLU ILE ALA GLY GLU GLU PHE ASN LEU SER SER THR SEQRES 21 A 605 LYS GLN LEU GLN THR ILE LEU PHE GLU LYS GLN GLY ILE SEQRES 22 A 605 LYS PRO LEU LYS LYS THR PRO GLY GLY ALA PRO SER THR SEQRES 23 A 605 SER GLU GLU VAL LEU GLU GLU LEU ALA LEU ASP TYR PRO SEQRES 24 A 605 LEU PRO LYS VAL ILE LEU GLU TYR ARG GLY LEU ALA LYS SEQRES 25 A 605 LEU LYS SER THR TYR THR ASP LYS LEU PRO LEU MET ILE SEQRES 26 A 605 ASN PRO LYS THR GLY ARG VAL HIS THR SER TYR HIS GLN SEQRES 27 A 605 ALA VAL THR ALA THR GLY ARG LEU SER SER THR ASP PRO SEQRES 28 A 605 ASN LEU GLN ASN ILE PRO VAL ARG ASN GLU GLU GLY ARG SEQRES 29 A 605 ARG ILE ARG GLN ALA PHE ILE ALA PRO GLU ASP TYR VAL SEQRES 30 A 605 ILE VAL SER ALA ASP TYR SER GLN ILE GLU LEU ARG ILE SEQRES 31 A 605 MET ALA HIS LEU SER ARG ASP LYS GLY LEU LEU THR ALA SEQRES 32 A 605 PHE ALA GLU GLY LYS ASP ILE HIS ARG ALA THR ALA ALA SEQRES 33 A 605 GLU VAL PHE GLY LEU PRO LEU GLU THR VAL THR SER GLU SEQRES 34 A 605 GLN ARG ARG SER ALA LYS ALA ILE ASN PHE GLY LEU ILE SEQRES 35 A 605 TYR GLY MET SER ALA PHE GLY LEU ALA ARG GLN LEU ASN SEQRES 36 A 605 ILE PRO ARG LYS GLU ALA GLN LYS TYR MET ASP LEU TYR SEQRES 37 A 605 PHE GLU ARG TYR PRO GLY VAL LEU GLU TYR MET GLU ARG SEQRES 38 A 605 THR ARG ALA GLN ALA LYS GLU GLN GLY TYR VAL GLU THR SEQRES 39 A 605 LEU ASP GLY ARG ARG LEU TYR LEU PRO ASP ILE LYS SER SEQRES 40 A 605 SER ASN GLY ALA ARG ARG ALA ALA ALA GLU ARG ALA ALA SEQRES 41 A 605 ILE ASN ALA PRO MET GLN GLY THR ALA ALA ASP ILE ILE SEQRES 42 A 605 LYS ARG ALA MET ILE ALA VAL ASP ALA TRP LEU GLN ALA SEQRES 43 A 605 GLU GLN PRO ARG VAL ARG MET ILE MET GLN VAL HIS ASP SEQRES 44 A 605 GLU LEU VAL PHE GLU VAL HIS LYS ASP ASP VAL ASP ALA SEQRES 45 A 605 VAL ALA LYS GLN ILE HIS GLN LEU MET GLU ASN CYS THR SEQRES 46 A 605 ARG LEU ASP VAL PRO LEU LEU VAL GLU VAL GLY SER GLY SEQRES 47 A 605 GLU ASN TRP ASP GLN ALA HIS HET MN B 2 1 HET ZN A 1 1 HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION FORMUL 3 MN MN 2+ FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *98(H2 O) HELIX 1 1 GLU A 336 LYS A 348 1 13 HELIX 2 2 ASN A 363 SER A 365 5 3 HELIX 3 3 ARG A 398 LEU A 409 1 12 HELIX 4 4 LEU A 421 TYR A 431 1 11 HELIX 5 5 THR A 442 LEU A 449 1 8 HELIX 6 6 MET A 458 TRP A 465 1 8 HELIX 7 7 PHE A 473 ALA A 477 1 5 HELIX 8 8 PHE A 486 GLN A 488 5 3 HELIX 9 9 LEU A 491 GLN A 517 1 27 HELIX 10 10 LYS A 520 ASN A 528 1 9 HELIX 11 11 GLU A 530 ASN A 543 1 14 HELIX 12 12 PRO A 549 ILE A 573 1 25 HELIX 13 13 GLN A 587 LEU A 590 1 4 HELIX 14 14 VAL A 613 LEU A 619 1 7 HELIX 15 15 LEU A 623 THR A 639 1 17 HELIX 16 16 LEU A 644 LEU A 646 5 3 HELIX 17 17 LEU A 676 ASN A 678 5 3 HELIX 18 18 GLU A 684 ALA A 692 1 9 HELIX 19 19 ILE A 709 SER A 718 1 10 HELIX 20 20 LYS A 721 ALA A 728 1 8 HELIX 21 21 ILE A 733 VAL A 741 1 9 HELIX 22 22 LEU A 746 THR A 748 5 3 HELIX 23 23 SER A 751 ILE A 765 1 15 HELIX 24 24 GLY A 772 LEU A 777 1 6 HELIX 25 25 ALA A 784 ARG A 794 1 11 HELIX 26 26 PRO A 796 GLN A 812 5 17 HELIX 27 27 PRO A 826 LYS A 829 5 4 HELIX 28 28 GLY A 833 GLU A 870 1 38 HELIX 29 29 VAL A 893 ASN A 906 1 14 SHEET 1 A 2 SER A 658 HIS A 660 0 SHEET 2 A 2 SER A 670 THR A 672 -1 N THR A 672 O SER A 658 SHEET 1 B 4 VAL A 916 GLY A 921 0 SHEET 2 B 4 TYR A 699 TYR A 706 -1 N ASP A 705 O GLU A 917 SHEET 3 B 4 GLU A 883 HIS A 889 -1 N VAL A 888 O VAL A 700 SHEET 4 B 4 VAL A 874 VAL A 880 -1 N VAL A 880 O GLU A 883 SHEET 1 C 2 TYR A 814 GLU A 816 0 SHEET 2 C 2 ARG A 822 TYR A 824 -1 N LEU A 823 O VAL A 815 SHEET 1 D 3 ALA A 353 THR A 358 0 SHEET 2 D 3 LEU A 368 GLU A 376 -1 N ALA A 374 O ALA A 353 SHEET 3 D 3 VAL A 379 PRO A 384 -1 N ILE A 383 O LEU A 371 SHEET 1 E 2 LYS A 416 GLY A 418 0 SHEET 2 E 2 ILE A 438 ASP A 441 1 N ALA A 439 O LYS A 416 LINK MN MN B 2 O3' DG B1007 1555 1555 2.63 LINK MN MN B 2 OP1 DC B1008 1555 1555 2.42 LINK MN MN B 2 OD1 ASP A 355 1555 1555 2.32 LINK OP1 DC B1008 ZN ZN A 1 1555 1555 2.03 LINK ZN ZN A 1 OD2 ASP A 355 1555 1555 1.97 LINK ZN ZN A 1 OE2 GLU A 357 1555 1555 2.16 LINK ZN ZN A 1 OD2 ASP A 501 1555 1555 1.94 CISPEP 1 ASP A 673 PRO A 674 0 -0.46 SITE 1 EXO 1 ASP A 355 SITE 1 AC1 5 ASP A 355 GLU A 357 ASP A 501 MN B 2 SITE 2 AC1 5 DC B1008 SITE 1 AC2 4 ZN A 1 ASP A 355 DG B1007 DC B1008 CRYST1 102.600 102.600 86.200 90.00 90.00 90.00 P 43 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 0.009747 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011601 0.00000