HEADER TRANSFERASE/DNA 24-FEB-10 3LWM TITLE STRUCTURE OF THE LARGE FRAGMENT OF THERMUS AQUATICUS DNA POLYMERASE I TITLE 2 IN COMPLEX WITH A BLUNT-ENDED DNA AND DDATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT, UNP RESIDUES 293-832; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC DNA; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC DNA KEYWDS DNA REPLICATION, DNA POLYMERASES, DNA-BINDING, DNA-DIRECTED DNA KEYWDS 2 POLYMERASE, AMINO ACID-TEMPLATING MECHANISM, NUCLEOTIDYLTRANSFERASE, KEYWDS 3 TRANSFERASE, TRANSFERASE-DNA COMPLEX, BLUNT-ENDED DNA, TEMPLATE- KEYWDS 4 INDEPENDENT DNA SYNTHESIS, TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE, KEYWDS 5 TEMPLATE-INDEPENDENT NUCLEOTIDE ADDITION EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 3 01-NOV-23 3LWM 1 REMARK LINK REVDAT 2 12-FEB-14 3LWM 1 JRNL VERSN REVDAT 1 05-MAY-10 3LWM 0 JRNL AUTH S.OBEID,N.BLATTER,R.KRANASTER,A.SCHNUR,K.DIEDERICHS,W.WELTE, JRNL AUTH 2 A.MARX JRNL TITL REPLICATION THROUGH AN ABASIC DNA LESION: STRUCTURAL BASIS JRNL TITL 2 FOR ADENINE SELECTIVITY JRNL REF EMBO J. V. 29 1738 2010 JRNL REFN ISSN 0261-4189 JRNL PMID 20400942 JRNL DOI 10.1038/EMBOJ.2010.64 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 32553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.4659 - 5.0027 1.00 2740 156 0.1621 0.1847 REMARK 3 2 5.0027 - 3.9714 1.00 2660 140 0.1521 0.1969 REMARK 3 3 3.9714 - 3.4696 1.00 2618 157 0.1607 0.2030 REMARK 3 4 3.4696 - 3.1524 1.00 2618 145 0.1774 0.2153 REMARK 3 5 3.1524 - 2.9265 1.00 2607 132 0.1840 0.2515 REMARK 3 6 2.9265 - 2.7540 1.00 2605 136 0.1970 0.2460 REMARK 3 7 2.7540 - 2.6161 1.00 2585 149 0.1991 0.2546 REMARK 3 8 2.6161 - 2.5022 1.00 2555 144 0.2035 0.2745 REMARK 3 9 2.5022 - 2.4059 1.00 2648 124 0.2124 0.2797 REMARK 3 10 2.4059 - 2.3229 1.00 2600 117 0.2265 0.2995 REMARK 3 11 2.3229 - 2.2502 0.98 2517 140 0.2424 0.3133 REMARK 3 12 2.2502 - 2.1859 0.83 2161 99 0.2608 0.3083 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 44.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.17600 REMARK 3 B22 (A**2) : 2.17600 REMARK 3 B33 (A**2) : -4.35200 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4986 REMARK 3 ANGLE : 0.851 6835 REMARK 3 CHIRALITY : 0.053 745 REMARK 3 PLANARITY : 0.003 806 REMARK 3 DIHEDRAL : 17.148 1917 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 295:627) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1337 -26.1597 -9.1061 REMARK 3 T TENSOR REMARK 3 T11: 0.1569 T22: 0.1560 REMARK 3 T33: 0.1390 T12: -0.0766 REMARK 3 T13: 0.0407 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 0.7156 L22: 1.0310 REMARK 3 L33: 1.4843 L12: 0.5479 REMARK 3 L13: -0.2393 L23: -0.5447 REMARK 3 S TENSOR REMARK 3 S11: -0.0890 S12: 0.1275 S13: -0.1115 REMARK 3 S21: -0.0437 S22: 0.0589 S23: -0.2013 REMARK 3 S31: -0.1513 S32: -0.1975 S33: 0.0019 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 628:697) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0350 -13.4529 -3.3222 REMARK 3 T TENSOR REMARK 3 T11: 0.5885 T22: 0.8823 REMARK 3 T33: 0.1705 T12: 0.3249 REMARK 3 T13: 0.0602 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 3.4787 L22: 3.4590 REMARK 3 L33: 0.0327 L12: -1.0148 REMARK 3 L13: 0.0221 L23: -0.3111 REMARK 3 S TENSOR REMARK 3 S11: -0.1548 S12: -0.3797 S13: 0.1756 REMARK 3 S21: 0.7460 S22: 0.4264 S23: -0.0369 REMARK 3 S31: -0.9634 S32: -0.5499 S33: -0.3272 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 698:832) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0360 -26.2055 -14.8654 REMARK 3 T TENSOR REMARK 3 T11: 0.1281 T22: 0.4171 REMARK 3 T33: 0.0508 T12: -0.0811 REMARK 3 T13: 0.0034 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.8626 L22: 0.6606 REMARK 3 L33: 1.2148 L12: 0.0973 REMARK 3 L13: 0.3335 L23: 0.1459 REMARK 3 S TENSOR REMARK 3 S11: -0.2000 S12: 0.2479 S13: -0.0482 REMARK 3 S21: -0.2465 S22: 0.2650 S23: 0.0372 REMARK 3 S31: -0.1045 S32: -0.6336 S33: -0.0911 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 101:112) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1607 -23.2186 4.2743 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.1830 REMARK 3 T33: 0.1609 T12: -0.0092 REMARK 3 T13: -0.0240 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.5249 L22: 2.4766 REMARK 3 L33: 2.6790 L12: -0.6845 REMARK 3 L13: 1.1578 L23: -2.4676 REMARK 3 S TENSOR REMARK 3 S11: 0.0342 S12: 0.3413 S13: -0.0504 REMARK 3 S21: 0.2826 S22: -0.2943 S23: -0.2316 REMARK 3 S31: -0.3927 S32: 0.2079 S33: 0.2459 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 204:216) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5396 -24.2659 5.6104 REMARK 3 T TENSOR REMARK 3 T11: 0.1546 T22: 0.2480 REMARK 3 T33: 0.1851 T12: 0.0565 REMARK 3 T13: -0.0400 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 2.6090 L22: 1.3929 REMARK 3 L33: 2.6524 L12: 1.3018 REMARK 3 L13: 1.3380 L23: 0.0126 REMARK 3 S TENSOR REMARK 3 S11: -0.3489 S12: -0.0128 S13: -0.3451 REMARK 3 S21: 0.0212 S22: 0.3084 S23: -0.2301 REMARK 3 S31: -0.1953 S32: 0.1377 S33: 0.0244 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) IN (+ REMARK 200 --+) GEOMETRY, AND A TOROIDAL REMARK 200 MIRROR (M2) REMARK 200 OPTICS : VERTICALLY COLLIMATING MIRROR REMARK 200 (M1, FOCUS AT INFINITY), REMARK 200 FOLLOWED BY A BARTELS REMARK 200 MONOCHROMATOR WITH DUAL CHANNEL REMARK 200 CUT CRYSTALS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32557 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.186 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.61 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9600 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) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.08 REMARK 200 R MERGE FOR SHELL (I) : 0.86400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.530 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.6_289 REMARK 200 STARTING MODEL: PDB ENTRY 3KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M TRIS HCL, PH 8, 0.2M AMMONIUM REMARK 280 CHLORIDE, 0.01M CALCIUM CHLORIDE AND 35% PEG 4000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 30.34567 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 60.69133 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 60.69133 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 30.34567 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: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C ACT A 3 LIES ON A SPECIAL POSITION. REMARK 375 CH3 ACT A 3 LIES ON A SPECIAL POSITION. 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 ALA A 293 REMARK 465 LEU A 294 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 VAL A 649 CG1 CG2 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 B 108 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 110 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -7.8 DEGREES REMARK 500 2DA B 112 O3' - P - OP1 ANGL. DEV. = 14.8 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 THR A 399 -169.86 -108.50 REMARK 500 VAL A 433 -67.98 -125.27 REMARK 500 ILE A 503 -69.03 -101.12 REMARK 500 HIS A 526 137.56 -175.70 REMARK 500 TYR A 545 -59.31 -124.34 REMARK 500 VAL A 586 -19.79 -165.73 REMARK 500 VAL A 649 178.50 174.45 REMARK 500 ARG A 651 36.74 -86.08 REMARK 500 ALA A 653 -113.32 -137.63 REMARK 500 ASP A 732 8.63 -64.62 REMARK 500 HIS A 784 -61.96 70.80 REMARK 500 TYR A 811 95.94 -168.84 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 835 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DDS A 1 O2A REMARK 620 2 DDS A 1 O3G 73.2 REMARK 620 3 DDS A 1 O1B 69.2 63.9 REMARK 620 4 HOH A 46 O 144.7 79.0 79.3 REMARK 620 5 HOH A 166 O 95.3 135.1 71.4 89.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDS A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 837 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3LWL RELATED DB: PDB DBREF 3LWM A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3LWM B 101 112 PDB 3LWM 3LWM 101 112 DBREF 3LWM C 205 216 PDB 3LWM 3LWM 205 216 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC 2DA SEQRES 1 C 12 DT DG DC DG DC DC DG DT DG DG DT DC MODRES 3LWM 2DA B 112 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA B 112 20 HET DDS A 1 29 HET ACT A 833 4 HET ACT A 2 4 HET ACT A 3 4 HET GOL A 834 6 HET GOL A 4 6 HET MG A 835 1 HET NA A 836 1 HET NA A 837 1 HET NA A 5 1 HET NA A 6 1 HET GOL B 2 6 HET GOL B 3 6 HET GOL B 1 6 HET ACT C 4 4 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM DDS 2',3'-DIDEOXYADENOSINE TRIPHOSPHATE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 2DA C10 H14 N5 O5 P FORMUL 4 DDS C10 H16 N5 O11 P3 FORMUL 5 ACT 4(C2 H3 O2 1-) FORMUL 8 GOL 5(C3 H8 O3) FORMUL 10 MG MG 2+ FORMUL 11 NA 4(NA 1+) FORMUL 19 HOH *154(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 HELIX 2 2 ARG A 343 LEU A 345 5 3 HELIX 3 3 LEU A 352 GLU A 363 1 12 HELIX 4 4 ASP A 372 ASP A 381 1 10 HELIX 5 5 THR A 386 GLY A 395 1 10 HELIX 6 6 GLU A 401 LEU A 420 1 20 HELIX 7 7 GLU A 423 VAL A 433 1 11 HELIX 8 8 VAL A 433 GLY A 448 1 16 HELIX 9 9 ASP A 452 GLY A 479 1 28 HELIX 10 10 SER A 486 ASP A 496 1 11 HELIX 11 11 SER A 515 LEU A 522 1 8 HELIX 12 12 HIS A 526 TYR A 545 1 20 HELIX 13 13 PRO A 548 ILE A 553 5 6 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 MET A 646 1 10 HELIX 18 18 ASP A 655 GLY A 672 1 18 HELIX 19 19 SER A 674 ALA A 683 1 10 HELIX 20 20 PRO A 685 PHE A 700 1 16 HELIX 21 21 PHE A 700 GLY A 718 1 19 HELIX 22 22 PRO A 731 ALA A 735 5 5 HELIX 23 23 VAL A 737 MET A 775 1 39 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 LYS A 831 1 6 SHEET 1 A 3 PHE A 306 LEU A 311 0 SHEET 2 A 3 LEU A 321 ARG A 328 -1 O ALA A 325 N GLY A 308 SHEET 3 A 3 ARG A 331 ARG A 334 -1 O HIS A 333 N ALA A 326 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 577 N ARG A 563 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 GLY A 824 N LEU A 606 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 2DA B 112 1555 1555 1.61 LINK O2A DDS A 1 MG MG A 835 1555 1555 2.11 LINK O3G DDS A 1 MG MG A 835 1555 1555 2.32 LINK O1B DDS A 1 MG MG A 835 1555 1555 2.39 LINK O HOH A 46 MG MG A 835 1555 1555 2.29 LINK O HOH A 166 MG MG A 835 1555 1555 2.11 CISPEP 1 TRP A 299 PRO A 300 0 3.16 CISPEP 2 ASP A 578 PRO A 579 0 1.63 CISPEP 3 VAL A 649 PRO A 650 0 -13.82 CISPEP 4 GLU A 652 ALA A 653 0 0.87 SITE 1 AC1 13 HOH A 46 HOH A 166 ARG A 587 GLN A 613 SITE 2 AC1 13 HIS A 639 ARG A 659 LYS A 663 PHE A 667 SITE 3 AC1 13 TYR A 671 MG A 835 HOH A 844 GOL B 1 SITE 4 AC1 13 2DA B 112 SITE 1 AC2 2 ARG A 313 ASP A 551 SITE 1 AC3 2 THR A 447 ARG A 778 SITE 1 AC4 3 LEU A 311 GLU A 400 ARG A 405 SITE 1 AC5 9 HOH A 141 HOH A 160 THR A 544 TYR A 545 SITE 2 AC5 9 PRO A 579 ASN A 580 ASN A 583 DC C 209 SITE 3 AC5 9 DC C 210 SITE 1 AC6 4 DDS A 1 HOH A 46 HOH A 166 ASP A 610 SITE 1 AC7 4 GLU A 615 TYR A 671 ASN A 750 GLN A 754 SITE 1 AC8 3 GLY A 510 ARG A 741 GLU A 745 SITE 1 AC9 1 GLU A 774 SITE 1 BC1 3 HOH A 112 LYS A 354 ASP A 355 SITE 1 BC2 6 HOH A 149 ARG A 536 LYS A 540 DG B 107 SITE 2 BC2 6 DG B 108 DC B 109 SITE 1 BC3 4 DG B 107 DG B 108 HOH C 9 DC C 209 SITE 1 BC4 6 DDS A 1 ASP A 610 GLU A 786 HOH A 843 SITE 2 BC4 6 HOH A 844 2DA B 112 SITE 1 BC5 2 DG C 206 DC C 207 CRYST1 109.592 109.592 91.037 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 0.009125 0.005268 0.000000 0.00000 SCALE2 0.000000 0.010536 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010985 0.00000