HEADER TRANSFERASE 05-OCT-15 5E41 TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH 5-(N-(10- TITLE 3 HYDROXYDECANOYL)-AMINOPENTENYL)-2'-DEOXYURIDINE-TRIPHOSPHATE 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*AP*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 10-JAN-24 5E41 1 LINK REVDAT 3 22-FEB-17 5E41 1 JRNL REVDAT 2 14-DEC-16 5E41 1 JRNL REVDAT 1 07-DEC-16 5E41 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_2165: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 55886 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2825 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 46.6832 - 4.8846 1.00 2814 161 0.1518 0.1810 REMARK 3 2 4.8846 - 3.8777 1.00 2702 141 0.1351 0.1849 REMARK 3 3 3.8777 - 3.3877 1.00 2679 159 0.1514 0.1926 REMARK 3 4 3.3877 - 3.0780 1.00 2660 149 0.1783 0.2301 REMARK 3 5 3.0780 - 2.8574 1.00 2671 137 0.2008 0.2673 REMARK 3 6 2.8574 - 2.6890 1.00 2657 137 0.2061 0.2369 REMARK 3 7 2.6890 - 2.5543 1.00 2637 148 0.2067 0.2915 REMARK 3 8 2.5543 - 2.4431 1.00 2651 150 0.2013 0.2618 REMARK 3 9 2.4431 - 2.3491 1.00 2666 126 0.2088 0.2693 REMARK 3 10 2.3491 - 2.2680 1.00 2652 123 0.2126 0.2816 REMARK 3 11 2.2680 - 2.1971 1.00 2621 140 0.2332 0.2729 REMARK 3 12 2.1971 - 2.1343 1.00 2665 128 0.2515 0.3136 REMARK 3 13 2.1343 - 2.0781 1.00 2666 121 0.2632 0.3076 REMARK 3 14 2.0781 - 2.0274 1.00 2608 137 0.3004 0.3250 REMARK 3 15 2.0274 - 1.9813 1.00 2651 145 0.3172 0.3385 REMARK 3 16 1.9813 - 1.9392 1.00 2617 147 0.3411 0.3633 REMARK 3 17 1.9392 - 1.9004 1.00 2604 138 0.3866 0.4074 REMARK 3 18 1.9004 - 1.8645 1.00 2626 140 0.4001 0.4212 REMARK 3 19 1.8645 - 1.8312 1.00 2632 142 0.4119 0.4208 REMARK 3 20 1.8312 - 1.8002 1.00 2582 156 0.4204 0.4299 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.970 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 : 0.006 5115 REMARK 3 ANGLE : 0.824 7041 REMARK 3 CHIRALITY : 0.047 768 REMARK 3 PLANARITY : 0.005 817 REMARK 3 DIHEDRAL : 15.623 3016 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): 39.0900 -40.8220 -18.3513 REMARK 3 T TENSOR REMARK 3 T11: 0.5266 T22: 0.3084 REMARK 3 T33: 0.4307 T12: -0.0774 REMARK 3 T13: 0.0917 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 1.3383 L22: 2.7157 REMARK 3 L33: 1.7796 L12: 0.1521 REMARK 3 L13: -0.0178 L23: 0.3570 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: 0.0839 S13: -0.3794 REMARK 3 S21: -0.3095 S22: -0.0067 S23: -0.3786 REMARK 3 S31: 0.5435 S32: 0.0512 S33: 0.0698 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.7040 -10.9479 1.5480 REMARK 3 T TENSOR REMARK 3 T11: 0.3808 T22: 0.2693 REMARK 3 T33: 0.3684 T12: -0.0621 REMARK 3 T13: 0.0174 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.6911 L22: 1.5293 REMARK 3 L33: 2.0437 L12: 0.5159 REMARK 3 L13: -0.1598 L23: 0.2717 REMARK 3 S TENSOR REMARK 3 S11: 0.0982 S12: -0.1942 S13: 0.2650 REMARK 3 S21: 0.1416 S22: -0.0583 S23: 0.0066 REMARK 3 S31: -0.2963 S32: 0.0183 S33: -0.0456 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 604 THROUGH 775 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4034 -22.0796 -7.2508 REMARK 3 T TENSOR REMARK 3 T11: 0.2983 T22: 0.6383 REMARK 3 T33: 0.3389 T12: 0.0112 REMARK 3 T13: 0.0002 T23: 0.0456 REMARK 3 L TENSOR REMARK 3 L11: 1.4475 L22: 1.5980 REMARK 3 L33: 4.3885 L12: 0.0925 REMARK 3 L13: -0.6017 L23: -0.7477 REMARK 3 S TENSOR REMARK 3 S11: -0.0775 S12: 0.0310 S13: 0.0758 REMARK 3 S21: 0.0805 S22: 0.2547 S23: 0.3660 REMARK 3 S31: -0.2638 S32: -1.2145 S33: -0.1421 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 776 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3170 -15.7312 -24.5371 REMARK 3 T TENSOR REMARK 3 T11: 0.5164 T22: 0.4419 REMARK 3 T33: 0.3194 T12: -0.0332 REMARK 3 T13: 0.0080 T23: 0.0755 REMARK 3 L TENSOR REMARK 3 L11: 4.0550 L22: 2.0457 REMARK 3 L33: 2.6556 L12: 1.3237 REMARK 3 L13: 0.5535 L23: -0.4929 REMARK 3 S TENSOR REMARK 3 S11: -0.0830 S12: 0.4985 S13: 0.3618 REMARK 3 S21: -0.3217 S22: 0.2166 S23: 0.1104 REMARK 3 S31: -0.5580 S32: -0.4253 S33: -0.1008 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.5979 -23.2180 5.1703 REMARK 3 T TENSOR REMARK 3 T11: 0.3941 T22: 0.4722 REMARK 3 T33: 0.4259 T12: -0.0611 REMARK 3 T13: 0.0040 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 2.5643 L22: 2.4137 REMARK 3 L33: 2.1964 L12: 0.5640 REMARK 3 L13: 0.4360 L23: -0.7756 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: 0.0183 S13: -0.3672 REMARK 3 S21: 0.2580 S22: -0.2060 S23: -0.2471 REMARK 3 S31: -0.1335 S32: 0.7275 S33: 0.2147 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3431 -20.8417 7.0021 REMARK 3 T TENSOR REMARK 3 T11: 0.5712 T22: 0.8424 REMARK 3 T33: 0.4627 T12: 0.0133 REMARK 3 T13: 0.0347 T23: -0.0705 REMARK 3 L TENSOR REMARK 3 L11: 2.2512 L22: 3.5873 REMARK 3 L33: 3.8103 L12: -0.7043 REMARK 3 L13: -0.0748 L23: 3.6128 REMARK 3 S TENSOR REMARK 3 S11: -0.1413 S12: -1.2625 S13: 0.9016 REMARK 3 S21: 1.0899 S22: 0.1871 S23: 0.1858 REMARK 3 S31: 0.0093 S32: -0.5643 S33: -0.0931 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.1350 -23.8385 5.9666 REMARK 3 T TENSOR REMARK 3 T11: 0.3915 T22: 0.3853 REMARK 3 T33: 0.3513 T12: -0.0716 REMARK 3 T13: -0.0125 T23: 0.0294 REMARK 3 L TENSOR REMARK 3 L11: 1.0030 L22: 1.4532 REMARK 3 L33: 0.7491 L12: -0.2945 REMARK 3 L13: -0.7691 L23: 0.8702 REMARK 3 S TENSOR REMARK 3 S11: -0.1358 S12: -0.3183 S13: -0.1112 REMARK 3 S21: 0.1903 S22: 0.2167 S23: -0.2631 REMARK 3 S31: 0.0805 S32: 0.1714 S33: -0.0932 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 5E41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : 55908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4100 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 (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M SODIUM CACODYLATE PH 6.5, 0.01M REMARK 280 MAGNESIUM ACETATE, 0.2M 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 29.87133 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 59.74267 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 59.74267 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 29.87133 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 HH11 ARG A 523 OE1 GLU A 530 1.58 REMARK 500 O HOH A 1004 O HOH A 1156 1.96 REMARK 500 O HOH B 209 O HOH B 228 1.98 REMARK 500 O HOH A 1039 O HOH A 1092 2.02 REMARK 500 O HOH A 1158 O HOH A 1201 2.04 REMARK 500 O HOH A 1195 O HOH A 1231 2.06 REMARK 500 O HOH A 1014 O HOH A 1228 2.09 REMARK 500 O HOH B 227 O HOH C 436 2.11 REMARK 500 O1 GOL A 904 O HOH A 1001 2.13 REMARK 500 O HOH C 428 O HOH C 436 2.14 REMARK 500 OE2 GLU A 537 O HOH A 1002 2.15 REMARK 500 O HOH C 424 O HOH C 436 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 O HOH A 1004 O HOH A 1128 6555 2.08 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. = 2.6 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.5 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 328 144.41 -171.91 REMARK 500 VAL A 433 -71.04 -122.78 REMARK 500 HIS A 526 137.32 -170.93 REMARK 500 TYR A 545 -58.24 -127.27 REMARK 500 VAL A 586 -18.96 -153.67 REMARK 500 HIS A 784 -59.09 72.00 REMARK 500 TYR A 811 89.98 -164.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1254 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1255 DISTANCE = 7.90 ANGSTROMS 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 AUL A 903 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 OD2 REMARK 620 2 ASP A 785 OD1 110.4 REMARK 620 3 AUL A 903 O2A 104.1 87.1 REMARK 620 4 HOH A1054 O 95.1 154.5 85.7 REMARK 620 5 HOH A1108 O 98.0 88.4 157.6 88.9 REMARK 620 N 1 2 3 4 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 OD1 REMARK 620 2 TYR A 611 O 78.6 REMARK 620 3 ASP A 785 OD2 92.8 92.3 REMARK 620 4 AUL A 903 O2A 102.0 179.1 88.3 REMARK 620 5 AUL A 903 O1B 163.8 92.6 101.2 86.7 REMARK 620 6 AUL A 903 O1G 84.4 87.8 177.1 91.7 81.7 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 AUL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 301 DBREF 5E41 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5E41 B 101 112 PDB 5E41 5E41 101 112 DBREF 5E41 C 201 216 PDB 5E41 5E41 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 DA 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 AUL A 903 84 HET GOL A 904 14 HET GOL A 905 14 HET GOL A 906 14 HET GOL C 301 14 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM AUL 2'-DEOXY-5-{(1E)-5-[(10-HYDROXYDECANOYL)AMINO]PENT-1- HETNAM 2 AUL EN-1-YL}URIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 MG 2(MG 2+) FORMUL 6 AUL C24 H42 N3 O16 P3 FORMUL 7 GOL 4(C3 H8 O3) FORMUL 11 HOH *325(H2 O) HELIX 1 AA1 GLU A 315 ALA A 319 5 5 HELIX 2 AA2 GLU A 337 ARG A 343 1 7 HELIX 3 AA3 LEU A 352 GLU A 363 1 12 HELIX 4 AA4 ASP A 372 ASP A 381 1 10 HELIX 5 AA5 THR A 386 GLY A 395 1 10 HELIX 6 AA6 GLU A 401 GLU A 421 1 21 HELIX 7 AA7 GLU A 423 VAL A 433 1 11 HELIX 8 AA8 VAL A 433 GLY A 448 1 16 HELIX 9 AA9 ASP A 452 GLY A 479 1 28 HELIX 10 AB1 SER A 486 ASP A 496 1 11 HELIX 11 AB2 SER A 515 LEU A 522 1 8 HELIX 12 AB3 PRO A 527 TYR A 545 1 19 HELIX 13 AB4 PRO A 548 ILE A 553 5 6 HELIX 14 AB5 THR A 588 ARG A 596 1 9 HELIX 15 AB6 GLN A 613 GLY A 624 1 12 HELIX 16 AB7 ASP A 625 GLU A 634 1 10 HELIX 17 AB8 ASP A 637 GLY A 648 1 12 HELIX 18 AB9 PRO A 650 VAL A 654 5 5 HELIX 19 AC1 ASP A 655 TYR A 671 1 17 HELIX 20 AC2 SER A 674 ALA A 683 1 10 HELIX 21 AC3 PRO A 685 SER A 699 1 15 HELIX 22 AC4 PRO A 701 GLY A 718 1 18 HELIX 23 AC5 PRO A 731 ALA A 735 5 5 HELIX 24 AC6 VAL A 737 MET A 775 1 39 HELIX 25 AC7 LYS A 793 GLY A 809 1 17 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 1.60 LINK OD2 ASP A 610 MG MG A 901 1555 1555 2.37 LINK OD1 ASP A 610 MG MG A 902 1555 1555 2.14 LINK O TYR A 611 MG MG A 902 1555 1555 2.15 LINK OD1 ASP A 785 MG MG A 901 1555 1555 2.20 LINK OD2 ASP A 785 MG MG A 902 1555 1555 1.97 LINK MG MG A 901 O2A AUL A 903 1555 1555 2.38 LINK MG MG A 901 O HOH A1054 1555 1555 2.61 LINK MG MG A 901 O HOH A1108 1555 1555 2.52 LINK MG MG A 902 O2A AUL A 903 1555 1555 1.99 LINK MG MG A 902 O1B AUL A 903 1555 1555 2.00 LINK MG MG A 902 O1G AUL A 903 1555 1555 2.05 CISPEP 1 TRP A 299 PRO A 300 0 -0.37 CISPEP 2 ASP A 578 PRO A 579 0 1.24 SITE 1 AC1 7 ASP A 610 ASP A 785 MG A 902 AUL A 903 SITE 2 AC1 7 HOH A1054 HOH A1108 DOC B 112 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 MG A 901 SITE 2 AC2 5 AUL A 903 SITE 1 AC3 24 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 2 AC3 24 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 3 AC3 24 HIS A 639 ARG A 659 ARG A 660 LYS A 663 SITE 4 AC3 24 THR A 664 PHE A 667 ASP A 785 MG A 901 SITE 5 AC3 24 MG A 902 HOH A1054 HOH A1058 HOH A1077 SITE 6 AC3 24 HOH A1115 DOC B 112 DA C 204 DG C 205 SITE 1 AC4 8 THR A 544 PRO A 579 ASN A 580 ASN A 583 SITE 2 AC4 8 HOH A1001 DC C 209 DC C 210 HOH C 423 SITE 1 AC5 4 GLU A 462 ARG A 593 GLU A 825 HOH A1050 SITE 1 AC6 5 LYS A 767 TYR A 811 HOH A1030 HOH A1056 SITE 2 AC6 5 HOH A1082 SITE 1 AC7 3 ARG A 728 DG C 206 DC C 207 CRYST1 107.774 107.774 89.614 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 0.009279 0.005357 0.000000 0.00000 SCALE2 0.000000 0.010714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011159 0.00000