HEADER TRANSFERASE/DNA 09-OCT-13 4N56 TITLE BINARY COMPLEX STRUCTURE OF KLENOW FRAGMENT OF TAQ DNA POLYMERASE TITLE 2 I707L MUTANT (CS3C KLENTAQ) WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PRIMER STRAND; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: TEMPLATE STRAND; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: KLENOW FRAGMENT (UNP RESIDUES 281-832); COMPND 15 SYNONYM: TAQ POLYMERASE 1; COMPND 16 EC: 2.7.7.7; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: 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: THERMUS AQUATICUS; SOURCE 7 ORGANISM_TAXID: 271; SOURCE 8 GENE: POLA, POL1; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, DNTP, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.Y.WU REVDAT 3 20-SEP-23 4N56 1 REMARK SEQADV LINK REVDAT 2 11-FEB-15 4N56 1 JRNL REVDAT 1 21-JAN-15 4N56 0 JRNL AUTH E.Y.WU,A.R.WALSH,E.C.MATERNE,E.P.HILTNER,B.ZIELINSKI, JRNL AUTH 2 B.R.MILLER,L.MAWBY,E.MODESTE,C.A.PARISH,W.M.BARNES, JRNL AUTH 3 M.B.KERMEKCHIEV JRNL TITL A CONSERVATIVE ISOLEUCINE TO LEUCINE MUTATION CAUSES MAJOR JRNL TITL 2 REARRANGEMENTS AND COLD SENSITIVITY IN KLENTAQ1 DNA JRNL TITL 3 POLYMERASE. JRNL REF BIOCHEMISTRY V. 54 881 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25537790 JRNL DOI 10.1021/BI501198F REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 32282 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 + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1615 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2196 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3850 REMARK 3 NUCLEIC ACID ATOMS : 552 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.293 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.796 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4550 ; 0.013 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 4155 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6279 ; 1.715 ; 1.871 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9529 ; 0.980 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 491 ; 6.843 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;31.793 ;22.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 664 ;19.437 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;19.867 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 680 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4744 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1038 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4N56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000082765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 11.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.73 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.68100 REMARK 200 FOR SHELL : 2.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 20 MM MANGANESE REMARK 280 CHLORIDE, 0.1 M SODIUM ACETATE, 10% W/V PEG4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 30.43000 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 60.86000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.86000 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 30.43000 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: 5660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 DA C 201 REMARK 465 MET A 280 REMARK 465 LEU A 281 REMARK 465 LEU A 282 REMARK 465 HIS A 283 REMARK 465 GLU A 284 REMARK 465 PHE A 285 REMARK 465 GLY A 286 REMARK 465 LEU A 287 REMARK 465 LEU A 288 REMARK 465 GLU A 289 REMARK 465 SER A 290 REMARK 465 PRO A 291 REMARK 465 LYS A 292 REMARK 465 ALA A 293 REMARK 465 ALA A 643 REMARK 465 SER A 644 REMARK 465 TRP A 645 REMARK 465 MET A 646 REMARK 465 PHE A 647 REMARK 465 GLY A 648 REMARK 465 VAL A 649 REMARK 465 PRO A 650 REMARK 465 ARG A 651 REMARK 465 GLU A 652 REMARK 465 ALA A 653 REMARK 465 VAL A 654 REMARK 465 ASP A 655 REMARK 465 PRO A 656 REMARK 465 LEU A 657 REMARK 465 MET A 658 REMARK 465 ARG A 659 REMARK 465 ARG A 660 REMARK 465 MET A 673 REMARK 465 SER A 674 REMARK 465 ALA A 675 REMARK 465 HIS A 676 REMARK 465 ARG A 677 REMARK 465 LEU A 678 REMARK 465 SER A 679 REMARK 465 GLN A 680 REMARK 465 GLU A 681 REMARK 465 LEU A 682 REMARK 465 ALA A 683 REMARK 465 ILE A 684 REMARK 465 PRO A 685 REMARK 465 TYR A 686 REMARK 465 GLU A 687 REMARK 465 GLU A 688 REMARK 465 ALA A 689 REMARK 465 GLN A 690 REMARK 465 ALA A 691 REMARK 465 PHE A 692 REMARK 465 ILE A 693 REMARK 465 GLU A 694 REMARK 465 ARG A 695 REMARK 465 TYR A 696 REMARK 465 PHE A 697 REMARK 465 GLN A 698 REMARK 465 SER A 699 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 LEU A 294 CG CD1 CD2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 296 CG CD OE1 OE2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 634 CG CD OE1 OE2 REMARK 470 ILE A 638 CG1 CG2 CD1 REMARK 470 LYS A 663 CG CD CE NZ REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 ARG A 716 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 774 CG CD OE1 OE2 REMARK 470 GLU A 794 CG CD OE1 OE2 REMARK 470 GLU A 805 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 B 111 O3' DOC B 112 P 0.102 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 DC B 111 C3' - O3' - P ANGL. DEV. = -9.5 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 8.1 DEGREES REMARK 500 DOC B 112 O3' - P - OP1 ANGL. DEV. = -14.4 DEGREES REMARK 500 DG C 204 O5' - C5' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG C 214 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 563 CG - CD - NE ANGL. DEV. = 13.0 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 ASP A 381 105.33 -166.00 REMARK 500 VAL A 433 -60.19 -130.19 REMARK 500 VAL A 586 -30.83 -150.82 REMARK 500 GLU A 601 151.66 -41.76 REMARK 500 GLN A 613 67.24 23.37 REMARK 500 THR A 664 37.79 -80.65 REMARK 500 ILE A 665 -36.54 -149.24 REMARK 500 HIS A 784 -71.03 76.06 REMARK 500 TYR A 811 95.81 -165.69 REMARK 500 LYS A 831 13.82 106.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 831 GLU A 832 149.54 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 C 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 204 OP2 REMARK 620 2 DG C 205 N7 93.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 GLU A 786 OE1 78.6 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 MN C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N5S RELATED DB: PDB REMARK 900 CS3C KLENTAQ-DNA COMPLEX WITH BOUND DCTP DBREF 4N56 A 281 832 UNP P19821 DPO1_THEAQ 281 832 DBREF 4N56 B 101 112 PDB 4N56 4N56 101 112 DBREF 4N56 C 201 216 PDB 4N56 4N56 201 216 SEQADV 4N56 MET A 280 UNP P19821 INITIATING METHIONINE SEQADV 4N56 LEU A 707 UNP P19821 ILE 707 ENGINEERED MUTATION SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DOC SEQRES 1 C 16 DA DA DA DG DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC SEQRES 1 A 553 MET LEU LEU HIS GLU PHE GLY LEU LEU GLU SER PRO LYS SEQRES 2 A 553 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 3 A 553 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 4 A 553 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 5 A 553 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 6 A 553 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 7 A 553 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 8 A 553 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 9 A 553 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 10 A 553 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 11 A 553 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 12 A 553 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 13 A 553 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 14 A 553 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 15 A 553 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 16 A 553 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 17 A 553 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 18 A 553 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 19 A 553 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 20 A 553 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 21 A 553 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 22 A 553 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 23 A 553 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 24 A 553 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 25 A 553 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 26 A 553 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 27 A 553 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 28 A 553 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 29 A 553 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 30 A 553 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 31 A 553 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 32 A 553 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 33 A 553 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP LEU GLU SEQRES 34 A 553 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 35 A 553 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 36 A 553 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 37 A 553 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 38 A 553 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 39 A 553 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 40 A 553 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 41 A 553 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 42 A 553 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 43 A 553 ASP TRP LEU SER ALA LYS GLU MODRES 4N56 DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET MN C 301 1 HET GOL A 901 6 HET MG A 902 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 DOC C9 H14 N3 O6 P FORMUL 4 MN MN 2+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 MG MG 2+ FORMUL 7 HOH *21(H2 O) HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 GLY A 395 1 10 HELIX 5 5 GLU A 401 LEU A 420 1 20 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 GLY A 479 1 28 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 LEU A 522 1 8 HELIX 11 11 ARG A 523 HIS A 526 5 4 HELIX 12 12 PRO A 527 TYR A 545 1 19 HELIX 13 13 LEU A 549 ILE A 553 5 5 HELIX 14 14 THR A 588 ARG A 596 1 9 HELIX 15 15 GLN A 613 GLY A 624 1 12 HELIX 16 16 ASP A 625 GLU A 634 1 10 HELIX 17 17 ASP A 637 THR A 642 1 6 HELIX 18 18 ALA A 662 PHE A 667 1 6 HELIX 19 19 PRO A 701 GLY A 718 1 18 HELIX 20 20 PRO A 731 ALA A 735 5 5 HELIX 21 21 VAL A 737 GLU A 774 1 38 HELIX 22 22 ARG A 795 GLY A 809 1 15 HELIX 23 23 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 296 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N PHE A 306 O ALA A 327 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.71 LINK OP2 DG C 204 MN MN C 301 1555 1555 1.86 LINK N7 DG C 205 MN MN C 301 1555 1555 2.65 LINK OD2 ASP A 610 MG MG A 902 1555 1555 2.47 LINK OE1 GLU A 786 MG MG A 902 1555 1555 2.20 CISPEP 1 TRP A 299 PRO A 300 0 0.95 CISPEP 2 ASP A 578 PRO A 579 0 1.75 SITE 1 AC1 2 DG C 204 DG C 205 SITE 1 AC2 6 THR A 544 PRO A 579 ASN A 580 ASN A 583 SITE 2 AC2 6 DC C 209 DC C 210 SITE 1 AC3 2 ASP A 610 GLU A 786 CRYST1 110.040 110.040 91.290 90.00 90.00 120.00 P 31 2 1 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 0.009088 0.005247 0.000000 0.00000 SCALE2 0.000000 0.010493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010954 0.00000