HEADER TRANSFERASE/DNA 18-JUL-11 3SZ2 TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN AN OPEN BINARY COMPLEX WITH DG AS TEMPLATING TITLE 3 NUCLEOBASE 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: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL I, POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: DNA SYNTHESIZER; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: DNA SYNTHESIZER KEYWDS DNA POLYMERASE, BINARY COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,A.MARX,K.DIEDERICHS REVDAT 4 13-SEP-23 3SZ2 1 REMARK LINK REVDAT 3 12-SEP-12 3SZ2 1 JRNL REVDAT 2 04-JUL-12 3SZ2 1 JRNL REVDAT 1 06-JUN-12 3SZ2 0 JRNL AUTH K.BETZ,D.A.MALYSHEV,T.LAVERGNE,W.WELTE,K.DIEDERICHS, JRNL AUTH 2 T.J.DWYER,P.ORDOUKHANIAN,F.E.ROMESBERG,A.MARX JRNL TITL KLENTAQ POLYMERASE REPLICATES UNNATURAL BASE PAIRS BY JRNL TITL 2 INDUCING A WATSON-CRICK GEOMETRY. JRNL REF NAT.CHEM.BIOL. V. 8 612 2012 JRNL REFN ISSN 1552-4450 JRNL PMID 22660438 JRNL DOI 10.1038/NCHEMBIO.966 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 64185 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3261 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 46.9489 - 6.1100 1.00 2642 154 0.1782 0.2181 REMARK 3 2 6.1100 - 4.8513 1.00 2647 147 0.1711 0.1919 REMARK 3 3 4.8513 - 4.2385 1.00 2677 121 0.1339 0.2198 REMARK 3 4 4.2385 - 3.8512 1.00 2612 170 0.1378 0.1633 REMARK 3 5 3.8512 - 3.5753 1.00 2619 173 0.1556 0.2108 REMARK 3 6 3.5753 - 3.3645 1.00 2653 145 0.1529 0.1883 REMARK 3 7 3.3645 - 3.1961 1.00 2603 140 0.1634 0.1958 REMARK 3 8 3.1961 - 3.0570 1.00 2685 154 0.1854 0.2242 REMARK 3 9 3.0570 - 2.9393 1.00 2664 114 0.2036 0.2686 REMARK 3 10 2.9393 - 2.8379 1.00 2635 157 0.2046 0.2557 REMARK 3 11 2.8379 - 2.7492 1.00 2633 160 0.2044 0.2647 REMARK 3 12 2.7492 - 2.6706 1.00 2662 130 0.2098 0.2582 REMARK 3 13 2.6706 - 2.6003 1.00 2626 149 0.2288 0.3389 REMARK 3 14 2.6003 - 2.5369 1.00 2668 147 0.2195 0.3249 REMARK 3 15 2.5369 - 2.4792 1.00 2626 157 0.2356 0.2991 REMARK 3 16 2.4792 - 2.4264 1.00 2651 134 0.2383 0.2961 REMARK 3 17 2.4264 - 2.3779 1.00 2686 127 0.2482 0.3465 REMARK 3 18 2.3779 - 2.3330 1.00 2678 113 0.2489 0.3472 REMARK 3 19 2.3330 - 2.2914 1.00 2670 127 0.2551 0.2921 REMARK 3 20 2.2914 - 2.2525 1.00 2616 141 0.2591 0.3032 REMARK 3 21 2.2525 - 2.2162 1.00 2642 137 0.2656 0.3038 REMARK 3 22 2.2162 - 2.1821 1.00 2662 111 0.2931 0.3434 REMARK 3 23 2.1821 - 2.1500 1.00 2667 153 0.3032 0.3264 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 36.85 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.640 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.100 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) : 2.90460 REMARK 3 B22 (A**2) : 2.90460 REMARK 3 B33 (A**2) : -5.80920 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 : 0.003 4897 REMARK 3 ANGLE : 0.758 6736 REMARK 3 CHIRALITY : 0.044 745 REMARK 3 PLANARITY : 0.003 791 REMARK 3 DIHEDRAL : 16.312 1887 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 293:450) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3133 -41.4881 -18.3571 REMARK 3 T TENSOR REMARK 3 T11: 0.2601 T22: 0.1809 REMARK 3 T33: 0.2181 T12: -0.0844 REMARK 3 T13: 0.0502 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 1.6181 L22: 2.3469 REMARK 3 L33: 1.3652 L12: -0.0786 REMARK 3 L13: 0.0178 L23: -0.0298 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: 0.0758 S13: -0.3285 REMARK 3 S21: -0.2777 S22: -0.0554 S23: -0.3044 REMARK 3 S31: 0.3495 S32: 0.0712 S33: 0.0377 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 451:634) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7488 -12.2738 -1.6518 REMARK 3 T TENSOR REMARK 3 T11: 0.2840 T22: 0.1933 REMARK 3 T33: 0.2207 T12: 0.0086 REMARK 3 T13: 0.0388 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 1.3358 L22: 1.2412 REMARK 3 L33: 1.6767 L12: 1.0885 REMARK 3 L13: -0.0679 L23: -0.0749 REMARK 3 S TENSOR REMARK 3 S11: 0.0727 S12: -0.0221 S13: 0.1812 REMARK 3 S21: 0.2187 S22: -0.0415 S23: 0.0799 REMARK 3 S31: -0.3915 S32: -0.2504 S33: -0.0037 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 635:697) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7291 -13.9529 -0.4545 REMARK 3 T TENSOR REMARK 3 T11: 1.1132 T22: 0.9248 REMARK 3 T33: 0.6418 T12: 0.5154 REMARK 3 T13: -0.0703 T23: -0.0412 REMARK 3 L TENSOR REMARK 3 L11: 3.3270 L22: 1.3915 REMARK 3 L33: 2.8066 L12: -1.1989 REMARK 3 L13: 0.0357 L23: 1.2247 REMARK 3 S TENSOR REMARK 3 S11: -0.5914 S12: -0.4819 S13: 0.6570 REMARK 3 S21: 0.6285 S22: 0.1949 S23: 0.3311 REMARK 3 S31: -1.9600 S32: -0.9424 S33: 0.1927 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 698:832) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7561 -25.8786 -14.7325 REMARK 3 T TENSOR REMARK 3 T11: -0.0316 T22: 0.3129 REMARK 3 T33: 0.1092 T12: -0.1383 REMARK 3 T13: 0.0159 T23: 0.0679 REMARK 3 L TENSOR REMARK 3 L11: 1.1104 L22: 0.9628 REMARK 3 L33: 2.4157 L12: 0.2155 REMARK 3 L13: -0.0161 L23: -0.2857 REMARK 3 S TENSOR REMARK 3 S11: -0.2098 S12: 0.0483 S13: 0.0790 REMARK 3 S21: -0.3557 S22: 0.2220 S23: 0.2343 REMARK 3 S31: -0.3620 S32: -0.8904 S33: -0.1051 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 101:111) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6138 -23.2906 5.1568 REMARK 3 T TENSOR REMARK 3 T11: 0.2769 T22: 0.3857 REMARK 3 T33: 0.3659 T12: 0.0493 REMARK 3 T13: -0.0720 T23: 0.0972 REMARK 3 L TENSOR REMARK 3 L11: 2.5745 L22: 0.1494 REMARK 3 L33: 0.0869 L12: 0.5261 REMARK 3 L13: -0.4113 L23: -0.0661 REMARK 3 S TENSOR REMARK 3 S11: 0.1299 S12: 0.1471 S13: -0.5745 REMARK 3 S21: 0.3550 S22: -0.4045 S23: -0.1989 REMARK 3 S31: 0.0981 S32: 0.7318 S33: 0.1433 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN D AND RESID 203:216) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9345 -23.7069 5.3434 REMARK 3 T TENSOR REMARK 3 T11: 0.2342 T22: 0.2735 REMARK 3 T33: 0.1697 T12: 0.0693 REMARK 3 T13: -0.0135 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.3945 L22: 3.9704 REMARK 3 L33: 4.1915 L12: 2.3312 REMARK 3 L13: 0.4222 L23: 0.2415 REMARK 3 S TENSOR REMARK 3 S11: -0.1595 S12: -0.2447 S13: 0.0248 REMARK 3 S21: 0.2922 S22: 0.0574 S23: -0.1614 REMARK 3 S31: 0.0350 S32: 0.0876 S33: 0.1952 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 3SZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000066830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.2300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 46.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER REMARK 200 TECHNIQUES REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000, 0.2M MGFORMATE, 0.1M REMARK 280 TRIS, PH 8.0, VAPOR DIFFUSION, HANGING 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 29.91733 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 59.83467 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 59.83467 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 29.91733 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: 6590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 HOH A 222 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 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 DA D 201 REMARK 465 DA D 202 REMARK 465 DA D 203 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 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 660 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 687 CG CD OE1 OE2 REMARK 470 GLU A 688 CG CD OE1 OE2 REMARK 470 ARG A 695 CG CD NE CZ NH1 NH2 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 OP2 DT D 215 O HOH D 151 2.02 REMARK 500 O HOH D 225 O HOH D 269 2.07 REMARK 500 O HOH D 224 O HOH D 269 2.10 REMARK 500 O HOH A 29 O HOH A 111 2.15 REMARK 500 O HOH A 124 O HOH A 202 2.16 REMARK 500 O HOH A 101 O HOH A 207 2.16 REMARK 500 O HOH D 223 O HOH D 269 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 469 OE1 GLU A 794 5554 2.11 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 DG B 108 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DDG B 112 O3' - P - OP1 ANGL. DEV. = -21.0 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 LEU A 294 -53.49 -129.82 REMARK 500 ARG A 328 140.45 -170.80 REMARK 500 GLU A 347 132.35 -170.20 REMARK 500 ASP A 381 110.52 -162.68 REMARK 500 THR A 399 -165.33 -102.56 REMARK 500 VAL A 433 -72.47 -124.67 REMARK 500 ILE A 503 -73.07 -116.13 REMARK 500 HIS A 526 142.95 174.98 REMARK 500 TYR A 545 -58.92 -125.11 REMARK 500 VAL A 586 -21.09 -158.77 REMARK 500 ILE A 638 -71.39 63.05 REMARK 500 ALA A 683 13.01 54.60 REMARK 500 PRO A 685 163.37 -49.57 REMARK 500 ASP A 732 6.51 -64.43 REMARK 500 HIS A 784 -64.67 76.53 REMARK 500 TYR A 811 86.20 -164.32 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 B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 2 O REMARK 620 2 HOH B 3 O 89.0 REMARK 620 3 HOH B 4 O 90.5 179.3 REMARK 620 4 HOH B 5 O 89.4 90.2 89.3 REMARK 620 5 HOH B 114 O 179.8 90.9 89.6 90.5 REMARK 620 6 HOH D 6 O 90.7 89.8 90.7 179.9 89.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 219 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3SV4 RELATED DB: PDB REMARK 900 RELATED ID: 3SV3 RELATED DB: PDB REMARK 900 RELATED ID: 3SYZ RELATED DB: PDB DBREF 3SZ2 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3SZ2 B 101 112 PDB 3SZ2 3SZ2 101 112 DBREF 3SZ2 D 201 216 PDB 3SZ2 3SZ2 201 216 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 DDG SEQRES 1 D 16 DA DA DA DG DC DG DC DG DC DC DG DT DG SEQRES 2 D 16 DG DT DC MODRES 3SZ2 DDG B 112 DG HET DDG B 112 21 HET FMT A 1 4 HET FMT A 833 3 HET FMT A 834 3 HET MG B 1 1 HET GOL D 1 14 HET FMT D 217 5 HET FMT D 218 3 HET FMT D 219 3 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM FMT FORMIC ACID HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 4 FMT 6(C H2 O2) FORMUL 7 MG MG 2+ FORMUL 8 GOL C3 H8 O3 FORMUL 12 HOH *295(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 ALA A 521 1 7 HELIX 12 12 PRO A 527 TYR A 545 1 19 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 655 PHE A 667 1 13 HELIX 18 18 SER A 674 LEU A 682 1 9 HELIX 19 19 PRO A 685 PHE A 700 1 16 HELIX 20 20 PHE A 700 GLY A 718 1 19 HELIX 21 21 PRO A 731 ALA A 735 5 5 HELIX 22 22 VAL A 737 GLU A 774 1 38 HELIX 23 23 LYS A 793 GLY A 809 1 17 HELIX 24 24 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 295 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N GLU A 295 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 GLY A 308 O ALA A 325 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 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 DDG B 112 1555 1555 1.60 LINK MG MG B 1 O HOH B 2 1555 1555 2.18 LINK MG MG B 1 O HOH B 3 1555 1555 2.18 LINK MG MG B 1 O HOH B 4 1555 1555 2.18 LINK MG MG B 1 O HOH B 5 1555 1555 2.18 LINK MG MG B 1 O HOH B 114 1555 1555 2.18 LINK MG MG B 1 O HOH D 6 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 1.02 CISPEP 2 ASP A 578 PRO A 579 0 -2.85 SITE 1 AC1 3 GLU A 462 ARG A 593 GLU A 825 SITE 1 AC2 3 SER A 739 GLU A 742 ARG A 746 SITE 1 AC3 6 TYR A 545 PRO A 579 ASN A 580 ASN A 583 SITE 2 AC3 6 DC D 209 FMT D 219 SITE 1 AC4 6 HOH B 2 HOH B 3 HOH B 4 HOH B 5 SITE 2 AC4 6 HOH B 114 HOH D 6 SITE 1 AC5 5 HOH A 198 HOH D 148 DC D 209 DC D 210 SITE 2 AC5 5 HOH D 256 SITE 1 AC6 7 HOH A 135 ASN A 485 ARG A 487 HOH B 221 SITE 2 AC6 7 HOH D 63 DG D 211 DT D 212 SITE 1 AC7 4 HOH D 193 DC D 205 DG D 206 HOH D 220 SITE 1 AC8 5 THR A 544 PRO A 579 FMT A 834 DC D 209 SITE 2 AC8 5 DC D 210 CRYST1 108.398 108.398 89.752 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 0.009225 0.005326 0.000000 0.00000 SCALE2 0.000000 0.010652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011142 0.00000