PDB Short entry for 1D9F HEADER TRANSFERASE/DNA, RNA 27-OCT-99 1D9F TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT TITLE 2 WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'- TITLE 3 D(TT)-AP(U)-D(T)-3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*TP*TP)-R(*(U31)P)-D(*T)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: URACIL HAS 3-AMINOPROPYL BOUND TO O2*; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA POLYMERASE I; COMPND 8 CHAIN: A; COMPND 9 FRAGMENT: KLENOW FRAGMENT; COMPND 10 SYNONYM: POL I, DNA DIRECTED DNA POLYMERASE; 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 KEYWDS KLENOW FRAGMENT, 2'-O-AMINOPROPYL NUCLEOTIDES, TRANSFERASE/DNA, RNA KEYWDS 2 COMPLEX, TRANSFERASE-DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.TEPLOVA,S.T.WALLACE,V.TERESHKO,G.MINASOV,A.M.SIMONS,P.D.COOK, AUTHOR 2 M.MANOHARAN,M.EGLI REVDAT 6 07-FEB-24 1D9F 1 REMARK REVDAT 5 03-NOV-21 1D9F 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1D9F 1 VERSN REVDAT 3 01-APR-03 1D9F 1 JRNL REVDAT 2 26-SEP-01 1D9F 3 ATOM CONECT REVDAT 1 02-DEC-99 1D9F 0 JRNL AUTH M.TEPLOVA,S.T.WALLACE,V.TERESHKO,G.MINASOV,A.M.SYMONS, JRNL AUTH 2 P.D.COOK,M.MANOHARAN,M.EGLI JRNL TITL STRUCTURAL ORIGINS OF THE EXONUCLEASE RESISTANCE OF A JRNL TITL 2 ZWITTERIONIC RNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 14240 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10588690 JRNL DOI 10.1073/PNAS.96.25.14240 REMARK 2 REMARK 2 RESOLUTION. 3.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 16291 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) : 0.224 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1622 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 : 4753 REMARK 3 NUCLEIC ACID ATOMS : 61 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 38 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) : -3.76900 REMARK 3 B22 (A**2) : -3.76900 REMARK 3 B33 (A**2) : 7.53700 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) : 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.630 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 1D9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99503 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20110 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.230 REMARK 200 R MERGE (I) : 0.07800 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, PH 6.4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 43.15000 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 64.72500 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 21.57500 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 DT B 1001 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 DT B1002 P OP1 OP2 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: 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 C7 DT B 1002 NZ LYS A 422 1.85 REMARK 500 C7 DT B 1002 NZ LYS A 422 1.85 REMARK 500 OD2 ASP A 362 OG SER A 365 2.14 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 DT B1002 O3' DT B1002 C3' -0.275 REMARK 500 DT B1002 C5 DT B1002 C7 -0.059 REMARK 500 DT B1002 C5 DT B1002 C7 -0.059 REMARK 500 DT B1004 O5' DT B1004 C5' 0.260 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 DT B1002 C2' - C3' - O3' ANGL. DEV. = -36.2 DEGREES REMARK 500 DT B1002 C3' - O3' - P ANGL. DEV. = -17.2 DEGREES REMARK 500 DT B1004 O5' - C5' - C4' ANGL. DEV. = 29.0 DEGREES REMARK 500 DT B1004 P - O5' - C5' ANGL. DEV. = 20.1 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 SER A 326 -164.55 -120.85 REMARK 500 ASN A 420 65.29 64.09 REMARK 500 ASN A 450 95.24 -171.15 REMARK 500 LEU A 516 0.85 -56.10 REMARK 500 ALA A 574 -140.60 -108.56 REMARK 500 GLU A 576 -176.31 64.05 REMARK 500 PHE A 578 149.91 -177.53 REMARK 500 LEU A 580 42.51 -100.44 REMARK 500 LYS A 584 -65.41 -154.28 REMARK 500 ILE A 589 -61.17 -103.27 REMARK 500 GLN A 594 124.72 91.99 REMARK 500 LYS A 597 -41.29 -19.22 REMARK 500 THR A 609 31.46 -83.43 REMARK 500 GLU A 611 71.34 -162.11 REMARK 500 ASP A 620 -46.63 -145.42 REMARK 500 GLN A 708 57.05 23.79 REMARK 500 LYS A 782 -10.28 62.86 REMARK 500 SER A 830 -30.89 -30.09 REMARK 500 SER A 831 -37.46 79.21 REMARK 500 PRO A 872 -179.61 -69.90 REMARK 500 HIS A 881 -122.99 50.92 REMARK 500 THR A 908 -117.82 -118.92 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B1004 OP1 REMARK 620 2 GLU A 357 OE2 134.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE 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 SO4 A 32 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 38 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 40 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 94 DBREF 1D9F A 324 928 UNP P00582 DPO1_ECOLI 324 928 DBREF 1D9F B 1001 1004 PDB 1D9F 1D9F 1001 1004 SEQADV 1D9F MET A 324 UNP P00582 VAL 324 ENGINEERED MUTATION SEQRES 1 B 4 DT DT U31 DT 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 MODRES 1D9F U31 B 1003 U HET U31 B1003 48 HET ZN A 1 1 HET SO4 A 32 5 HET SO4 A 38 5 HET SO4 A 40 5 HET SO4 A 94 5 HETNAM U31 2'-O-3-AMINOPROPYL 2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 1 U31 C12 H20 N3 O9 P FORMUL 3 ZN ZN 2+ FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 HOH *38(H2 O) HELIX 1 1 ASP A 335 ALA A 349 1 15 HELIX 2 2 SER A 397 GLU A 410 1 14 HELIX 3 3 ASN A 420 ASN A 430 1 11 HELIX 4 4 THR A 442 ASN A 450 1 9 HELIX 5 5 ASP A 457 LYS A 467 1 11 HELIX 6 6 THR A 472 GLY A 478 1 7 HELIX 7 7 LYS A 479 GLN A 483 5 5 HELIX 8 8 THR A 485 ILE A 489 5 5 HELIX 9 9 ALA A 490 LEU A 516 1 27 HELIX 10 10 HIS A 519 ILE A 529 1 11 HELIX 11 11 ILE A 529 GLY A 544 1 16 HELIX 12 12 ASP A 548 ALA A 574 1 27 HELIX 13 13 LEU A 586 PHE A 591 1 6 HELIX 14 14 PRO A 607 GLU A 611 5 5 HELIX 15 15 GLU A 612 ALA A 618 1 7 HELIX 16 16 TYR A 621 TYR A 640 1 20 HELIX 17 17 LYS A 643 ILE A 648 5 6 HELIX 18 18 ASN A 675 ILE A 679 5 5 HELIX 19 19 ASN A 683 GLN A 691 1 9 HELIX 20 20 GLN A 708 SER A 718 1 11 HELIX 21 21 ASP A 720 GLU A 729 1 10 HELIX 22 22 ASP A 732 PHE A 742 1 11 HELIX 23 23 THR A 750 TYR A 766 1 17 HELIX 24 24 SER A 769 ASN A 778 1 10 HELIX 25 25 GLU A 783 TYR A 795 1 13 HELIX 26 26 TYR A 795 GLY A 813 1 19 HELIX 27 27 PRO A 826 SER A 830 5 5 HELIX 28 28 ASN A 832 GLN A 871 1 40 HELIX 29 29 ASP A 892 CYS A 907 1 16 HELIX 30 30 ASN A 923 HIS A 928 1 6 SHEET 1 A 6 VAL A 331 THR A 332 0 SHEET 2 A 6 VAL A 379 PRO A 384 1 O ALA A 380 N VAL A 331 SHEET 3 A 6 LEU A 368 GLU A 376 -1 O LEU A 371 N ILE A 383 SHEET 4 A 6 PHE A 352 THR A 358 -1 N ALA A 353 O ALA A 374 SHEET 5 A 6 LYS A 416 GLY A 418 1 O VAL A 417 N PHE A 354 SHEET 6 A 6 ILE A 438 ASP A 441 1 N ALA A 439 O LYS A 416 SHEET 1 B 2 SER A 658 HIS A 660 0 SHEET 2 B 2 SER A 670 THR A 672 -1 O SER A 670 N HIS A 660 SHEET 1 C 4 VAL A 874 VAL A 880 0 SHEET 2 C 4 GLU A 883 HIS A 889 -1 N GLU A 883 O VAL A 880 SHEET 3 C 4 TYR A 699 TYR A 706 -1 N VAL A 700 O VAL A 888 SHEET 4 C 4 VAL A 916 GLY A 921 -1 N GLU A 917 O ASP A 705 SHEET 1 D 2 TYR A 814 GLU A 816 0 SHEET 2 D 2 ARG A 822 TYR A 824 -1 N LEU A 823 O VAL A 815 LINK O3'A DT B1002 P AU31 B1003 1555 1555 1.59 LINK O3'B DT B1002 P BU31 B1003 1555 1555 1.59 LINK O3'AU31 B1003 P A DT B1004 1555 1555 1.63 LINK O3'BU31 B1003 P B DT B1004 1555 1555 1.62 LINK OP1A DT B1004 ZN ZN A 1 1555 1555 2.49 LINK ZN ZN A 1 OE2 GLU A 357 1555 1555 2.02 CISPEP 1 ASP A 673 PRO A 674 0 -0.10 SITE 1 AC1 5 ASP A 355 GLU A 357 TYR A 497 ASP A 501 SITE 2 AC1 5 DT B1004 SITE 1 AC2 3 HIS A 519 LYS A 520 ARG A 822 SITE 1 AC3 3 ARG A 682 ARG A 754 LYS A 758 SITE 1 AC4 3 ARG A 436 GLY A 437 ILE A 438 SITE 1 AC5 2 LYS A 340 ARG A 400 CRYST1 102.650 102.650 86.300 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 0.009742 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011587 0.00000