HEADER NUCLEOTIDYLTRANSFERASE 11-AUG-87 1DPI TITLE STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I TITLE 2 COMPLEXED WITH D/TMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I KLENOW FRAGMENT; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: T7; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: T7; SOURCE 7 EXPRESSION_SYSTEM_GENE: T7 KEYWDS NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR L.BEESE,D.OLLIS,T.STEITZ REVDAT 4 07-FEB-24 1DPI 1 REMARK REVDAT 3 24-FEB-09 1DPI 1 VERSN REVDAT 2 01-APR-03 1DPI 1 JRNL REVDAT 1 16-OCT-87 1DPI 0 JRNL AUTH D.L.OLLIS,P.BRICK,R.HAMLIN,N.G.XUONG,T.A.STEITZ JRNL TITL STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA JRNL TITL 2 POLYMERASE I COMPLEXED WITH DTMP. JRNL REF NATURE V. 313 762 1985 JRNL REFN ISSN 0028-0836 JRNL PMID 3883192 JRNL DOI 10.1038/313762A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.L.OLLIS,C.KLINE,T.A.STEITZ REMARK 1 TITL DOMAIN OF E. COLI DNA POLYMERASE I SHOWING SEQUENCE HOMOLOGY REMARK 1 TITL 2 TO T7 DNA POLYMERASE REMARK 1 REF NATURE V. 313 818 1985 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.BRICK,D.OLLIS,T.A.STEITZ REMARK 1 TITL CRYSTALLIZATION AND 7 ANGSTROMS RESOLUTION ELECTRON DENSITY REMARK 1 TITL 2 MAP OF THE LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE REMARK 1 TITL 3 I REMARK 1 REF J.MOL.BIOL. V. 166 453 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.M.JOYCE,W.S.KELLEY,N.D.F.GRINDLEY REMARK 1 TITL NUCLEOTIDE SEQUENCE OF THE ESCHERICHIA COLI POLA GENE AND REMARK 1 TITL 2 PRIMARY STRUCTURE OF DNA POLYMERASE I REMARK 1 REF J.BIOL.CHEM. V. 257 1958 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 4 REMARK 1 AUTH W.E.BROWN,K.H.STUMP,W.S.KELLEY REMARK 1 TITL ESCHERICHIA COLI DNA POLYMERASE I. SEQUENCE CHARACTERIZATION REMARK 1 TITL 2 AND SECONDARY STRUCTURE PREDICTION REMARK 1 REF J.BIOL.CHEM. V. 257 1965 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 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 FIT/AGREEMENT OF MODEL WITH ALL DATA. 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 : 546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DPI 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_1000172888. 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 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 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 (%): 63.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 42.90000 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 64.35000 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 21.45000 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 VAL A 324 REMARK 465 ILE A 325 REMARK 465 ALA A 574 REMARK 465 GLY A 575 REMARK 465 GLU A 576 REMARK 465 GLU A 577 REMARK 465 PHE A 578 REMARK 465 ASN A 579 REMARK 465 LEU A 580 REMARK 465 SER A 581 REMARK 465 SER A 582 REMARK 465 THR A 583 REMARK 465 LYS A 584 REMARK 465 GLN A 585 REMARK 465 LEU A 586 REMARK 465 GLN A 587 REMARK 465 THR A 588 REMARK 465 ILE A 589 REMARK 465 LEU A 590 REMARK 465 PHE A 591 REMARK 465 GLU A 592 REMARK 465 LYS A 593 REMARK 465 GLN A 594 REMARK 465 GLY A 595 REMARK 465 ILE A 596 REMARK 465 LYS A 597 REMARK 465 PRO A 598 REMARK 465 LEU A 599 REMARK 465 LYS A 600 REMARK 465 LYS A 601 REMARK 465 THR A 602 REMARK 465 PRO A 603 REMARK 465 GLY A 604 REMARK 465 GLY A 605 REMARK 465 ALA A 606 REMARK 465 PRO A 607 REMARK 465 SER A 608 REMARK 465 THR A 609 REMARK 465 SER A 610 REMARK 465 GLU A 611 REMARK 465 GLU A 612 REMARK 465 VAL A 613 REMARK 465 LEU A 614 REMARK 465 GLU A 615 REMARK 465 GLU A 616 REMARK 465 LEU A 617 REMARK 465 ALA A 618 REMARK 465 LEU A 619 REMARK 465 ASP A 620 REMARK 465 TYR A 621 REMARK 465 PRO A 622 REMARK 465 PRO A 780 REMARK 465 ARG A 781 REMARK 465 LYS A 782 REMARK 465 GLU A 783 REMARK 465 ALA A 784 REMARK 465 GLN A 785 REMARK 465 LYS A 786 REMARK 465 TYR A 787 DBREF 1DPI A 324 928 UNP P00582 DPO1_ECOLI 324 928 SEQRES 1 A 605 VAL 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 ZN A 1 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ CRYST1 102.900 102.900 85.800 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 0.009718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011655 0.00000