HEADER TRANSFERASE 15-AUG-16 5SZT TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH 7-(N-(10- TITLE 3 HYDROXYDECANOYL)-AMINOPENTENYL)-7-DEAZA-2'-DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 13 3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS LINKER-MODIFIED NUCLEOTIDE, KLENTAQ, DNA POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.HOTTIN,K.BETZ,A.MARX REVDAT 4 17-JAN-24 5SZT 1 REMARK LINK REVDAT 3 16-OCT-19 5SZT 1 REMARK REVDAT 2 22-FEB-17 5SZT 1 JRNL REVDAT 1 14-DEC-16 5SZT 0 JRNL AUTH A.HOTTIN,K.BETZ,K.DIEDERICHS,A.MARX JRNL TITL STRUCTURAL BASIS FOR THE KLENTAQ DNA POLYMERASE CATALYSED JRNL TITL 2 INCORPORATION OF ALKENE- VERSUS ALKYNE-MODIFIED NUCLEOTIDES. JRNL REF CHEMISTRY V. 23 2109 2017 JRNL REFN ISSN 1521-3765 JRNL PMID 27901305 JRNL DOI 10.1002/CHEM.201604515 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2443) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 57294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2894 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 46.9654 - 4.9632 1.00 2741 156 0.1694 0.1922 REMARK 3 2 4.9632 - 3.9401 1.00 2642 139 0.1383 0.1861 REMARK 3 3 3.9401 - 3.4422 1.00 2622 158 0.1627 0.1937 REMARK 3 4 3.4422 - 3.1275 1.00 2606 144 0.1754 0.1985 REMARK 3 5 3.1275 - 2.9034 1.00 2606 132 0.1936 0.2263 REMARK 3 6 2.9034 - 2.7322 1.00 2595 137 0.1965 0.2217 REMARK 3 7 2.7322 - 2.5954 1.00 2584 146 0.1984 0.2314 REMARK 3 8 2.5954 - 2.4825 1.00 2561 145 0.2017 0.2809 REMARK 3 9 2.4825 - 2.3869 1.00 2606 126 0.2121 0.2618 REMARK 3 10 2.3869 - 2.3045 1.00 2613 115 0.2115 0.2993 REMARK 3 11 2.3045 - 2.2325 1.00 2561 141 0.2265 0.3027 REMARK 3 12 2.2325 - 2.1687 1.00 2583 118 0.2332 0.3181 REMARK 3 13 2.1687 - 2.1116 1.00 2581 121 0.2311 0.2610 REMARK 3 14 2.1116 - 2.0600 1.00 2583 132 0.2588 0.2895 REMARK 3 15 2.0600 - 2.0132 1.00 2555 138 0.2740 0.2936 REMARK 3 16 2.0132 - 1.9704 1.00 2559 146 0.2957 0.3101 REMARK 3 17 1.9704 - 1.9310 1.00 2567 139 0.3183 0.3515 REMARK 3 18 1.9310 - 1.8945 1.00 2566 140 0.3462 0.3986 REMARK 3 19 1.8945 - 1.8607 1.00 2552 128 0.3546 0.3466 REMARK 3 20 1.8607 - 1.8291 1.00 2574 152 0.3808 0.3841 REMARK 3 21 1.8291 - 1.7996 1.00 2543 141 0.3996 0.3833 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 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 5228 REMARK 3 ANGLE : 0.634 7209 REMARK 3 CHIRALITY : 0.041 776 REMARK 3 PLANARITY : 0.003 871 REMARK 3 DIHEDRAL : 18.157 3105 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 293 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2369 -41.0134 -18.2185 REMARK 3 T TENSOR REMARK 3 T11: 0.5104 T22: 0.3225 REMARK 3 T33: 0.4471 T12: -0.1032 REMARK 3 T13: 0.0945 T23: -0.0397 REMARK 3 L TENSOR REMARK 3 L11: 1.2189 L22: 2.1691 REMARK 3 L33: 1.6994 L12: -0.4172 REMARK 3 L13: -0.1161 L23: 0.2103 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: 0.0327 S13: -0.3981 REMARK 3 S21: -0.2261 S22: -0.0225 S23: -0.3241 REMARK 3 S31: 0.4850 S32: 0.0302 S33: 0.0595 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9026 -10.8093 1.4273 REMARK 3 T TENSOR REMARK 3 T11: 0.3539 T22: 0.2282 REMARK 3 T33: 0.3175 T12: -0.0362 REMARK 3 T13: 0.0271 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.2503 L22: 1.6586 REMARK 3 L33: 3.0219 L12: 0.7722 REMARK 3 L13: -0.2261 L23: 0.0517 REMARK 3 S TENSOR REMARK 3 S11: 0.1231 S12: -0.1371 S13: 0.1907 REMARK 3 S21: 0.1479 S22: -0.0575 S23: 0.0476 REMARK 3 S31: -0.6614 S32: 0.0165 S33: -0.0560 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 604 THROUGH 775 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4862 -22.3974 -7.5443 REMARK 3 T TENSOR REMARK 3 T11: 0.2882 T22: 0.7692 REMARK 3 T33: 0.3302 T12: 0.0435 REMARK 3 T13: -0.0115 T23: 0.0508 REMARK 3 L TENSOR REMARK 3 L11: 1.2671 L22: 1.8284 REMARK 3 L33: 3.4467 L12: 0.3206 REMARK 3 L13: -0.3105 L23: -0.8240 REMARK 3 S TENSOR REMARK 3 S11: -0.0813 S12: -0.0472 S13: 0.0127 REMARK 3 S21: 0.0763 S22: 0.2672 S23: 0.3522 REMARK 3 S31: -0.3181 S32: -1.3019 S33: -0.1250 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 776 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2248 -15.9511 -24.8686 REMARK 3 T TENSOR REMARK 3 T11: 0.4672 T22: 0.4400 REMARK 3 T33: 0.2915 T12: -0.0280 REMARK 3 T13: -0.0010 T23: 0.0457 REMARK 3 L TENSOR REMARK 3 L11: 4.1308 L22: 2.2292 REMARK 3 L33: 3.0807 L12: 1.5052 REMARK 3 L13: -0.4315 L23: -0.4500 REMARK 3 S TENSOR REMARK 3 S11: -0.0974 S12: 0.5145 S13: 0.2831 REMARK 3 S21: -0.3048 S22: 0.1831 S23: 0.0630 REMARK 3 S31: -0.4151 S32: -0.5422 S33: -0.0917 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8865 -23.2375 5.2894 REMARK 3 T TENSOR REMARK 3 T11: 0.3889 T22: 0.3742 REMARK 3 T33: 0.4632 T12: 0.0046 REMARK 3 T13: 0.0274 T23: 0.0365 REMARK 3 L TENSOR REMARK 3 L11: 2.8957 L22: 1.6928 REMARK 3 L33: 2.1451 L12: -0.2570 REMARK 3 L13: 1.7819 L23: -1.1113 REMARK 3 S TENSOR REMARK 3 S11: 0.0301 S12: 0.3477 S13: -0.3836 REMARK 3 S21: 0.2888 S22: -0.2886 S23: -0.1010 REMARK 3 S31: -0.0023 S32: 0.6206 S33: 0.2344 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2714 -21.2072 7.1997 REMARK 3 T TENSOR REMARK 3 T11: 0.5687 T22: 0.8422 REMARK 3 T33: 0.4160 T12: -0.0151 REMARK 3 T13: 0.0079 T23: -0.0490 REMARK 3 L TENSOR REMARK 3 L11: 5.4964 L22: 2.6286 REMARK 3 L33: 4.1263 L12: -0.7561 REMARK 3 L13: 0.8809 L23: 0.7378 REMARK 3 S TENSOR REMARK 3 S11: -0.1433 S12: -1.2364 S13: 0.4220 REMARK 3 S21: 1.0657 S22: -0.5079 S23: 0.0915 REMARK 3 S31: -0.2816 S32: -0.9723 S33: 0.4797 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2773 -23.8203 5.9964 REMARK 3 T TENSOR REMARK 3 T11: 0.3264 T22: 0.3183 REMARK 3 T33: 0.3967 T12: -0.0409 REMARK 3 T13: -0.0424 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 1.6050 L22: 2.3432 REMARK 3 L33: 1.4107 L12: 0.0576 REMARK 3 L13: -1.0961 L23: 1.2163 REMARK 3 S TENSOR REMARK 3 S11: -0.0538 S12: -0.1449 S13: -0.3713 REMARK 3 S21: 0.3444 S22: 0.3064 S23: -0.5192 REMARK 3 S31: 0.0217 S32: 0.3789 S33: -0.2987 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 5SZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000220841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.000000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3M8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M SODIUM CACODYLATE PH 6.5, 0.01 REMARK 280 M MAGNESIUM ACETATE, 0.2 M AMMONIUM ACETATE, 30% PEG 4000, VAPOR REMARK 280 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 30.20500 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 60.41000 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 60.41000 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 30.20500 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: 7440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 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 OE2 GLU A 473 HH21 ARG A 476 1.56 REMARK 500 HH TYR A 729 O HOH A 1007 1.58 REMARK 500 O HOH C 407 O HOH C 410 1.98 REMARK 500 O HIS A 526 O HOH A 1001 2.08 REMARK 500 O HOH A 1113 O HOH A 1162 2.13 REMARK 500 O HOH C 411 O HOH C 421 2.13 REMARK 500 NH1 ARG A 411 O HOH A 1002 2.17 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 O HOH A 1106 O HOH A 1163 6555 2.18 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. = 2.5 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 111 C3' - O3' - P ANGL. DEV. = -9.0 DEGREES REMARK 500 DOC B 112 O3' - P - OP2 ANGL. DEV. = 8.6 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 ARG A 328 142.87 -171.13 REMARK 500 VAL A 433 -71.85 -126.94 REMARK 500 HIS A 526 140.00 -170.11 REMARK 500 TYR A 545 -57.38 -129.41 REMARK 500 VAL A 586 -30.96 -156.99 REMARK 500 HIS A 784 -60.75 73.69 REMARK 500 TYR A 811 92.71 -166.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 72J A 907 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 77.2 REMARK 620 3 ASP A 785 OD2 87.0 91.1 REMARK 620 4 72J A 907 O2B 168.9 92.3 96.7 REMARK 620 5 72J A 907 O2B 168.9 92.2 96.5 0.2 REMARK 620 6 72J A 907 O1A 102.5 176.7 85.6 88.2 88.3 REMARK 620 7 72J A 907 O1A 103.0 176.2 85.1 87.7 87.8 0.7 REMARK 620 8 72J A 907 O3G 89.7 87.0 176.4 86.3 86.5 96.4 96.8 REMARK 620 9 72J A 907 O2G 92.5 86.8 177.8 83.4 83.6 96.6 97.0 2.9 REMARK 620 N 1 2 3 4 5 6 7 8 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 ASP A 785 OD1 107.3 REMARK 620 3 72J A 907 O1A 100.4 82.3 REMARK 620 4 72J A 907 O1A 100.2 81.5 0.8 REMARK 620 5 HOH A1064 O 100.8 93.6 158.7 158.9 REMARK 620 6 HOH A1084 O 91.5 159.1 85.6 86.5 91.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 301 O REMARK 620 2 HOH B 313 O 90.1 REMARK 620 3 HOH B 315 O 90.0 90.1 REMARK 620 4 HOH B 322 O 179.9 90.0 90.0 REMARK 620 5 HOH B 323 O 90.0 179.6 90.2 89.9 REMARK 620 6 HOH C 430 O 89.8 89.8 179.8 90.2 89.8 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 MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 72J A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 302 DBREF 5SZT A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5SZT B 101 112 PDB 5SZT 5SZT 101 112 DBREF 5SZT C 201 216 PDB 5SZT 5SZT 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 DOC SEQRES 1 C 16 DA DA DA DT DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET DOC B 112 30 HET MG A 901 1 HET MG A 902 1 HET GOL A 903 14 HET ACT A 904 7 HET ACT A 905 7 HET ACT A 906 7 HET 72J A 907 176 HET MG B 201 1 HET GOL C 301 14 HET ACT C 302 7 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETNAM 72J 7-(N-(10-HYDROXYDECANOYL)-AMINOPENTENYL)-7-DEAZA-2'- HETNAM 2 72J DATP HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 MG 3(MG 2+) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 10 72J C26 H44 N5 O14 P3 FORMUL 14 HOH *250(H2 O) HELIX 1 AA1 GLU A 337 ARG A 343 1 7 HELIX 2 AA2 LEU A 352 GLU A 363 1 12 HELIX 3 AA3 ASP A 372 ASP A 381 1 10 HELIX 4 AA4 THR A 386 GLY A 395 1 10 HELIX 5 AA5 GLU A 401 LEU A 420 1 20 HELIX 6 AA6 GLU A 423 VAL A 433 1 11 HELIX 7 AA7 VAL A 433 GLY A 448 1 16 HELIX 8 AA8 ASP A 452 GLY A 479 1 28 HELIX 9 AA9 SER A 486 ASP A 496 1 11 HELIX 10 AB1 SER A 515 LEU A 522 1 8 HELIX 11 AB2 PRO A 527 TYR A 545 1 19 HELIX 12 AB3 PRO A 548 ILE A 553 5 6 HELIX 13 AB4 THR A 588 ARG A 596 1 9 HELIX 14 AB5 GLN A 613 GLY A 624 1 12 HELIX 15 AB6 ASP A 625 GLU A 634 1 10 HELIX 16 AB7 ASP A 637 GLY A 648 1 12 HELIX 17 AB8 PRO A 650 VAL A 654 5 5 HELIX 18 AB9 ASP A 655 TYR A 671 1 17 HELIX 19 AC1 SER A 674 LEU A 682 1 9 HELIX 20 AC2 PRO A 685 SER A 699 1 15 HELIX 21 AC3 PRO A 701 GLY A 718 1 18 HELIX 22 AC4 PRO A 731 ALA A 735 5 5 HELIX 23 AC5 VAL A 737 MET A 775 1 39 HELIX 24 AC6 ARG A 795 GLY A 809 1 15 HELIX 25 AC7 LEU A 828 GLU A 832 5 5 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLU A 820 N ASP A 610 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 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 1.56 LINK OD1 ASP A 610 MG MG A 901 1555 1555 2.10 LINK OD2 ASP A 610 MG MG A 902 1555 1555 2.30 LINK O TYR A 611 MG MG A 901 1555 1555 2.18 LINK OD2 ASP A 785 MG MG A 901 1555 1555 2.00 LINK OD1 ASP A 785 MG MG A 902 1555 1555 2.15 LINK MG MG A 901 O2BA72J A 907 1555 1555 2.04 LINK MG MG A 901 O2BB72J A 907 1555 1555 2.05 LINK MG MG A 901 O1AA72J A 907 1555 1555 2.04 LINK MG MG A 901 O1AB72J A 907 1555 1555 2.01 LINK MG MG A 901 O3GB72J A 907 1555 1555 1.98 LINK MG MG A 901 O2GA72J A 907 1555 1555 1.94 LINK MG MG A 902 O1AA72J A 907 1555 1555 2.42 LINK MG MG A 902 O1AB72J A 907 1555 1555 2.44 LINK MG MG A 902 O HOH A1064 1555 1555 2.29 LINK MG MG A 902 O HOH A1084 1555 1555 2.55 LINK MG MG B 201 O HOH B 301 1555 1555 2.18 LINK MG MG B 201 O HOH B 313 1555 1555 2.18 LINK MG MG B 201 O HOH B 315 1555 1555 2.18 LINK MG MG B 201 O HOH B 322 1555 1555 2.18 LINK MG MG B 201 O HOH B 323 1555 1555 2.18 LINK MG MG B 201 O HOH C 430 1555 1555 2.18 CISPEP 1 TRP A 299 PRO A 300 0 4.09 CISPEP 2 ASP A 578 PRO A 579 0 0.86 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MG A 902 SITE 2 AC1 5 72J A 907 SITE 1 AC2 7 ASP A 610 ASP A 785 MG A 901 72J A 907 SITE 2 AC2 7 HOH A1064 HOH A1084 DOC B 112 SITE 1 AC3 10 THR A 544 TYR A 545 PRO A 579 ASN A 580 SITE 2 AC3 10 ASN A 583 HOH A1010 HOH A1016 DC C 209 SITE 3 AC3 10 DC C 210 HOH C 416 SITE 1 AC4 3 ARG A 313 TRP A 318 LEU A 552 SITE 1 AC5 1 PHE A 724 SITE 1 AC6 2 ASP A 371 ARG A 435 SITE 1 AC7 24 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 2 AC7 24 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 3 AC7 24 HIS A 639 ARG A 659 ARG A 660 LYS A 663 SITE 4 AC7 24 THR A 664 PHE A 667 ASP A 785 MG A 901 SITE 5 AC7 24 MG A 902 HOH A1018 HOH A1080 HOH A1084 SITE 6 AC7 24 HOH A1145 DOC B 112 DT C 204 DG C 205 SITE 1 AC8 6 HOH B 301 HOH B 313 HOH B 315 HOH B 322 SITE 2 AC8 6 HOH B 323 HOH C 430 SITE 1 AC9 3 DG C 205 DG C 206 HOH C 407 SITE 1 AD1 2 DG C 206 DC C 207 CRYST1 108.425 108.425 90.615 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 0.009223 0.005325 0.000000 0.00000 SCALE2 0.000000 0.010650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011036 0.00000