HEADER TRANSFERASE/DNA 28-JAN-11 3AU6 TITLE DNA POLYMERASE X FROM THERMUS THERMOPHILUS HB8 TERNARY COMPLEX WITH TITLE 2 PRIMER/TEMPLATE DNA AND DDGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA FAMILY (X FAMILY); COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3'; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3'; COMPND 12 CHAIN: T; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: POLX, TTHA1150; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-11A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS RSGI, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, POLXC DOMAIN, PHP DOMAIN, DNA POLYMERASE, DRP LYASE, AP KEYWDS 3 ENDONUCLEASE, DNA REPAIR, DNA BINDING, NUCLEOTIDE BINDING, KEYWDS 4 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.NAKANE,R.MASUI,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 13-MAR-24 3AU6 1 REMARK LINK REVDAT 2 25-DEC-13 3AU6 1 JRNL REVDAT 1 25-JAN-12 3AU6 0 JRNL AUTH S.NAKANE,H.ISHIKAWA,N.NAKAGAWA,S.KURAMITSU,R.MASUI JRNL TITL THE STRUCTURAL BASIS OF THE KINETIC MECHANISM OF A JRNL TITL 2 GAP-FILLING X-FAMILY DNA POLYMERASE THAT BINDS MG(2+)-DNTP JRNL TITL 3 BEFORE BINDING TO DNA. JRNL REF J.MOL.BIOL. V. 417 179 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22306405 JRNL DOI 10.1016/J.JMB.2012.01.025 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.5.0110 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 13885 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) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 685 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 914 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4425 REMARK 3 NUCLEIC ACID ATOMS : 346 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.96000 REMARK 3 B22 (A**2) : 3.96000 REMARK 3 B33 (A**2) : -7.93000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.651 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.601 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.643 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4935 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3371 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6745 ; 1.631 ; 2.087 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8178 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 7.452 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;36.654 ;22.967 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 798 ;21.936 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;16.266 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 736 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5205 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 964 ; 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): 2791 ; 0.531 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1139 ; 0.062 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4460 ; 0.997 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2144 ; 1.067 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2285 ; 1.876 ; 4.500 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 : 1.40 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 U VALUES REMARK 4 REMARK 4 3AU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000029698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13997 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 76.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL (PH 8.5), 25MM MGSO4 REMARK 280 7H2O, 1.8M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 134.27750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.08300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.08300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 201.41625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.08300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.08300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.13875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.08300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.08300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 201.41625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.08300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.08300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.13875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 134.27750 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 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 GLY A 128 REMARK 465 ASP A 129 REMARK 465 LEU A 130 REMARK 465 THR A 131 REMARK 465 ARG A 132 REMARK 465 LEU A 133 REMARK 465 LYS A 134 REMARK 465 ALA A 381 REMARK 465 GLY A 382 REMARK 465 ARG A 572 REMARK 465 ARG A 573 REMARK 465 GLY A 574 REMARK 465 VAL A 575 REMARK 465 DC T 1 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 OD2 ASP A 200 MG MG A 577 1.55 REMARK 500 O1G DG3 A 576 MG MG A 577 1.57 REMARK 500 OG1 THR A 470 OD1 ASP A 508 1.98 REMARK 500 O TYR A 503 O ARG A 506 2.14 REMARK 500 N ASP A 316 OE1 GLU A 319 2.18 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 DC P 1 O3' DC P 1 C3' -0.048 REMARK 500 DT P 6 O3' DDG P 7 P -0.114 REMARK 500 DC T 4 O3' DC T 4 C3' -0.048 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 DA P 2 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA P 2 N1 - C6 - N6 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT P 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT P 4 N3 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT P 4 C5 - C4 - O4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA P 5 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT P 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DDG P 7 O3' - P - O5' ANGL. DEV. = -33.6 DEGREES REMARK 500 DDG P 7 O3' - P - OP2 ANGL. DEV. = 14.6 DEGREES REMARK 500 DG T 2 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG T 2 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DC T 4 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC T 5 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC T 5 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DT T 7 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DA T 8 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DC T 9 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DT T 10 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = 2.2 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 ASN A 23 120.69 -20.43 REMARK 500 GLU A 45 -59.57 -23.26 REMARK 500 LYS A 50 32.88 -169.47 REMARK 500 GLU A 67 -7.21 -57.95 REMARK 500 LEU A 70 -76.62 -61.48 REMARK 500 PHE A 72 -76.82 -83.41 REMARK 500 VAL A 101 -97.65 -84.91 REMARK 500 PRO A 103 -77.42 -23.55 REMARK 500 PHE A 136 -84.39 -58.75 REMARK 500 ALA A 149 -76.66 -58.62 REMARK 500 LYS A 156 -14.70 75.37 REMARK 500 VAL A 163 -19.92 -144.30 REMARK 500 CYS A 186 -152.81 -122.66 REMARK 500 ALA A 211 -81.24 -63.80 REMARK 500 LYS A 222 -97.06 -81.68 REMARK 500 ALA A 232 139.10 -178.91 REMARK 500 GLU A 295 -54.04 -18.18 REMARK 500 TRP A 308 113.82 -30.59 REMARK 500 PRO A 311 -66.15 -27.64 REMARK 500 ASP A 316 67.75 60.08 REMARK 500 PRO A 335 -62.90 -29.76 REMARK 500 GLN A 342 112.86 166.82 REMARK 500 SER A 348 -154.28 -152.65 REMARK 500 VAL A 371 67.11 -106.20 REMARK 500 ALA A 377 37.14 -66.00 REMARK 500 VAL A 378 -60.14 -130.35 REMARK 500 ARG A 379 57.33 -104.28 REMARK 500 ARG A 430 -38.66 -29.73 REMARK 500 ARG A 442 84.66 24.93 REMARK 500 LEU A 458 -8.40 -55.50 REMARK 500 HIS A 464 -73.39 -96.41 REMARK 500 HIS A 468 78.66 -5.21 REMARK 500 ALA A 471 -3.11 68.36 REMARK 500 ARG A 476 -30.24 -140.32 REMARK 500 PRO A 479 163.57 -46.23 REMARK 500 GLU A 485 -62.17 -26.56 REMARK 500 MET A 507 58.65 -141.33 REMARK 500 ASP A 511 -72.26 -18.78 REMARK 500 PHE A 538 22.40 -65.08 REMARK 500 ARG A 555 37.55 74.56 REMARK 500 TYR A 562 -71.87 -8.28 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 MG A 577 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 188 OG REMARK 620 2 DG3 A 576 O3A 117.2 REMARK 620 3 DG3 A 576 O1A 144.1 57.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 578 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 198 OD2 REMARK 620 2 ASP A 200 OD1 71.3 REMARK 620 3 DG3 A 576 O1A 76.9 94.4 REMARK 620 4 DG3 A 576 O5' 113.4 69.6 55.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 579 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 413 OE2 REMARK 620 2 HIS A 468 NE2 67.0 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 DG3 A 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 577 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 578 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 579 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 580 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 581 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 582 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 584 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AU2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CA-DGTP REMARK 900 RELATED ID: TTK003000748.1 RELATED DB: TARGETDB DBREF 3AU6 A 1 575 UNP Q5SJ64 Q5SJ64_THET8 1 575 DBREF 3AU6 P 1 7 PDB 3AU6 3AU6 1 7 DBREF 3AU6 T 1 11 PDB 3AU6 3AU6 1 11 SEQRES 1 A 575 MET ARG ASN GLN GLU LEU ALA ARG ILE PHE GLU GLU ILE SEQRES 2 A 575 GLY LEU MET SER GLU PHE LEU GLY ASP ASN PRO PHE ARG SEQRES 3 A 575 VAL ARG ALA TYR HIS GLN ALA ALA ARG THR LEU TYR ASP SEQRES 4 A 575 LEU ASP THR PRO ILE GLU GLU ILE ALA GLU LYS GLY LYS SEQRES 5 A 575 GLU ALA LEU MET GLU LEU PRO GLY VAL GLY PRO ASP LEU SEQRES 6 A 575 ALA GLU LYS ILE LEU GLU PHE LEU ARG THR GLY LYS VAL SEQRES 7 A 575 ARG LYS HIS GLU GLU LEU SER ARG LYS VAL PRO ARG GLY SEQRES 8 A 575 VAL LEU GLU VAL MET GLU VAL PRO GLY VAL GLY PRO LYS SEQRES 9 A 575 THR ALA ARG LEU LEU TYR GLU GLY LEU GLY ILE ASP SER SEQRES 10 A 575 LEU GLU LYS LEU LYS ALA ALA LEU ASP ARG GLY ASP LEU SEQRES 11 A 575 THR ARG LEU LYS GLY PHE GLY PRO LYS ARG ALA GLU ARG SEQRES 12 A 575 ILE ARG GLU GLY LEU ALA LEU ALA GLN ALA ALA GLY LYS SEQRES 13 A 575 ARG ARG PRO LEU GLY ALA VAL LEU SER LEU ALA ARG SER SEQRES 14 A 575 LEU LEU GLU ALA ILE ARG ALA LEU PRO GLY VAL GLU ARG SEQRES 15 A 575 ALA GLU LEU CYS GLY SER ALA ARG ARG TYR LYS ASP THR SEQRES 16 A 575 VAL GLY ASP LEU ASP PHE LEU VAL ALA SER ARG GLU GLY SEQRES 17 A 575 GLU ARG ALA VAL GLU GLY PHE VAL ARG LEU PRO GLN VAL SEQRES 18 A 575 LYS GLU VAL TYR ALA LYS GLY LYS GLU ARG ALA THR VAL SEQRES 19 A 575 PHE LEU LYS ASN GLY LEU GLN VAL ASP LEU ARG VAL VAL SEQRES 20 A 575 PRO PRO GLU SER TYR GLY ALA GLY LEU GLN TYR LEU THR SEQRES 21 A 575 GLY SER LYS ALA HIS SER ILE ARG LEU ARG ALA LEU ALA SEQRES 22 A 575 GLN GLU LYS GLY LEU LYS LEU SER GLU TYR GLY VAL PHE SEQRES 23 A 575 ARG GLY GLU LYS ARG ILE ALA GLY GLU THR GLU GLU GLU SEQRES 24 A 575 VAL TYR ALA ALA LEU GLY LEU PRO TRP ILE PRO PRO PRO SEQRES 25 A 575 LEU ARG GLU ASP GLN GLY GLU VAL GLU ALA ALA LEU GLU SEQRES 26 A 575 GLY ARG LEU PRO LYS LEU LEU GLU LEU PRO GLN VAL LYS SEQRES 27 A 575 GLY ASP LEU GLN VAL HIS SER THR TYR SER ASP GLY GLN SEQRES 28 A 575 ASN THR LEU GLU GLU LEU TRP GLU ALA ALA LYS THR MET SEQRES 29 A 575 GLY TYR ARG TYR LEU ALA VAL THR ASP HIS SER PRO ALA SEQRES 30 A 575 VAL ARG VAL ALA GLY GLY PRO SER PRO GLU GLU ALA LEU SEQRES 31 A 575 LYS ARG VAL GLY GLU ILE ARG ARG PHE ASN GLU THR HIS SEQRES 32 A 575 GLY PRO PRO TYR LEU LEU ALA GLY ALA GLU VAL ASP ILE SEQRES 33 A 575 HIS PRO ASP GLY THR LEU ASP TYR PRO ASP TRP VAL LEU SEQRES 34 A 575 ARG GLU LEU ASP LEU VAL LEU VAL SER VAL HIS SER ARG SEQRES 35 A 575 PHE ASN LEU PRO LYS ALA ASP GLN THR LYS ARG LEU LEU SEQRES 36 A 575 LYS ALA LEU GLU ASN PRO PHE VAL HIS VAL LEU ALA HIS SEQRES 37 A 575 PRO THR ALA ARG LEU LEU GLY ARG ARG ALA PRO ILE GLU SEQRES 38 A 575 ALA ASP TRP GLU ALA VAL PHE GLN LYS ALA LYS GLU LYS SEQRES 39 A 575 GLY VAL ALA VAL GLU ILE ASP GLY TYR TYR ASP ARG MET SEQRES 40 A 575 ASP LEU PRO ASP ASP LEU ALA ARG MET ALA TYR GLY MET SEQRES 41 A 575 GLY LEU TRP ILE SER LEU SER THR ASP ALA HIS GLN THR SEQRES 42 A 575 ASP HIS LEU ARG PHE MET GLU LEU ALA VAL GLY THR ALA SEQRES 43 A 575 GLN ARG ALA TRP ILE GLY PRO GLU ARG VAL LEU ASN THR SEQRES 44 A 575 LEU ASP TYR GLU ASP LEU LEU SER TRP LEU LYS ALA ARG SEQRES 45 A 575 ARG GLY VAL SEQRES 1 P 7 DC DA DG DT DA DT DDG SEQRES 1 T 11 DC DG DG DC DC DA DT DA DC DT DG MODRES 3AU6 DDG P 7 DG HET DDG P 7 21 HET DG3 A 576 30 HET MG A 577 1 HET MG A 578 1 HET ZN A 579 1 HET CL A 580 1 HET CL A 581 1 HET CL A 582 1 HET CL A 583 1 HET SO4 A 584 5 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 4 DG3 C10 H16 N5 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 ZN ZN 2+ FORMUL 8 CL 4(CL 1-) FORMUL 12 SO4 O4 S 2- FORMUL 13 HOH *26(H2 O) HELIX 1 1 ARG A 2 GLY A 21 1 20 HELIX 2 2 ASN A 23 TYR A 38 1 16 HELIX 3 3 PRO A 43 GLU A 49 1 7 HELIX 4 4 GLY A 62 ARG A 74 1 13 HELIX 5 5 VAL A 78 VAL A 88 1 11 HELIX 6 6 PRO A 89 GLU A 97 1 9 HELIX 7 7 GLY A 102 GLY A 114 1 13 HELIX 8 8 SER A 117 ASP A 126 1 10 HELIX 9 9 GLY A 137 GLY A 155 1 19 HELIX 10 10 VAL A 163 ALA A 176 1 14 HELIX 11 11 CYS A 186 ARG A 191 1 6 HELIX 12 12 ARG A 210 VAL A 216 1 7 HELIX 13 13 PRO A 248 GLU A 250 5 3 HELIX 14 14 SER A 251 GLY A 261 1 11 HELIX 15 15 SER A 262 LYS A 276 1 15 HELIX 16 16 THR A 296 LEU A 304 1 9 HELIX 17 17 PRO A 310 ARG A 314 5 5 HELIX 18 18 GLY A 318 LEU A 324 1 7 HELIX 19 19 GLU A 333 VAL A 337 5 5 HELIX 20 20 THR A 353 GLY A 365 1 13 HELIX 21 21 SER A 385 GLU A 401 1 17 HELIX 22 22 PRO A 425 ARG A 430 1 6 HELIX 23 23 PRO A 446 LEU A 458 1 13 HELIX 24 24 ASP A 483 GLU A 493 1 11 HELIX 25 25 PRO A 510 GLY A 519 1 10 HELIX 26 26 GLN A 532 ARG A 537 5 6 HELIX 27 27 PHE A 538 ALA A 549 1 12 HELIX 28 28 VAL A 556 LEU A 560 5 5 HELIX 29 29 ASP A 561 ALA A 571 1 11 SHEET 1 A 2 ARG A 158 PRO A 159 0 SHEET 2 A 2 THR A 195 VAL A 196 -1 O VAL A 196 N ARG A 158 SHEET 1 B 4 LEU A 199 LEU A 202 0 SHEET 2 B 4 GLN A 241 ARG A 245 1 O GLN A 241 N LEU A 199 SHEET 3 B 4 ARG A 231 LEU A 236 -1 N VAL A 234 O VAL A 242 SHEET 4 B 4 VAL A 221 ALA A 226 -1 N GLU A 223 O PHE A 235 SHEET 1 C 3 LYS A 279 LEU A 280 0 SHEET 2 C 3 VAL A 285 ARG A 287 -1 O PHE A 286 N LYS A 279 SHEET 3 C 3 LYS A 290 ALA A 293 -1 O ILE A 292 N VAL A 285 SHEET 1 D 3 GLY A 339 ASP A 340 0 SHEET 2 D 3 TYR A 368 ALA A 370 1 O ALA A 370 N ASP A 340 SHEET 3 D 3 TYR A 407 LEU A 409 1 O LEU A 409 N LEU A 369 SHEET 1 E 6 ASP A 373 HIS A 374 0 SHEET 2 E 6 GLY A 411 VAL A 414 1 O GLU A 413 N ASP A 373 SHEET 3 E 6 LEU A 434 VAL A 437 1 O LEU A 436 N ALA A 412 SHEET 4 E 6 VAL A 465 LEU A 466 1 O VAL A 465 N VAL A 435 SHEET 5 E 6 ALA A 497 ASP A 501 1 O GLU A 499 N LEU A 466 SHEET 6 E 6 ILE A 524 SER A 527 1 O SER A 525 N VAL A 498 LINK O3' DT P 6 P DDG P 7 1555 1555 1.49 LINK OG SER A 188 MG MG A 577 1555 1555 2.89 LINK OD2 ASP A 198 MG MG A 578 1555 1555 2.34 LINK OD1 ASP A 200 MG MG A 578 1555 1555 2.53 LINK OE2 GLU A 413 ZN ZN A 579 1555 1555 2.38 LINK NE2 HIS A 468 ZN ZN A 579 1555 1555 2.31 LINK O3A DG3 A 576 MG MG A 577 1555 1555 1.96 LINK O1A DG3 A 576 MG MG A 577 1555 1555 2.95 LINK O1A DG3 A 576 MG MG A 578 1555 1555 1.88 LINK O5' DG3 A 576 MG MG A 578 1555 1555 2.93 CISPEP 1 GLY A 261 SER A 262 0 -7.16 CISPEP 2 GLY A 383 PRO A 384 0 -7.77 CISPEP 3 PRO A 405 PRO A 406 0 2.87 CISPEP 4 ASP A 508 LEU A 509 0 -16.22 SITE 1 AC1 16 ARG A 157 GLY A 187 SER A 188 ARG A 191 SITE 2 AC1 16 VAL A 196 GLY A 197 ASP A 198 ASP A 200 SITE 3 AC1 16 TYR A 258 GLY A 261 LYS A 263 ARG A 270 SITE 4 AC1 16 MG A 577 MG A 578 DDG P 7 DC T 4 SITE 1 AC2 4 SER A 188 ASP A 198 ASP A 200 DG3 A 576 SITE 1 AC3 4 ASP A 198 ASP A 200 ASP A 243 DG3 A 576 SITE 1 AC4 4 GLU A 413 HIS A 440 HIS A 468 ASP A 529 SITE 1 AC5 1 LYS A 193 SITE 1 AC6 2 ARG A 107 ASP A 426 SITE 1 AC7 1 LYS A 338 SITE 1 AC8 3 HIS A 440 PHE A 443 ARG A 477 CRYST1 80.166 80.166 268.555 90.00 90.00 90.00 P 43 21 2 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 0.012474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003724 0.00000