HEADER TRANSFERASE/DNA 06-FEB-12 4DLG TITLE TERNARY STRUCTURE OF THE LARGE FRAGMENT OF TAQ DNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 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 PRIMER; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA TEMPLATE; 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 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS DNA POLYMERASE, TERNARY COMPLEX, A FAMILY, DNA SYNTHESIS, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID,B.HOLZBERGER REVDAT 2 13-SEP-23 4DLG 1 REMARK LINK REVDAT 1 28-NOV-12 4DLG 0 JRNL AUTH B.HOLZBERGER,S.OBEID,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL STRUCTURAL INSIGHTS INTO THE POTENTIAL OF 4-FLUOROPROLINE TO JRNL TITL 2 MODULATE BIOPHYSICAL PROPERTIES OF PROTEIN JRNL REF CHEM SCI V. 3 2924 2012 JRNL REFN ISSN 2041-6520 JRNL DOI 10.1039/C2SC20545A REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 47964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4647 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 46.6860 - 5.8800 1.00 2932 169 0.1729 0.2095 REMARK 3 2 5.8800 - 4.6685 1.00 2899 155 0.1651 0.2064 REMARK 3 3 4.6685 - 4.0788 1.00 2964 158 0.1442 0.1920 REMARK 3 4 4.0788 - 3.7060 1.00 2896 177 0.1648 0.1849 REMARK 3 5 3.7060 - 3.4405 1.00 2910 182 0.1713 0.2116 REMARK 3 6 3.4405 - 3.2377 1.00 2940 150 0.1865 0.2178 REMARK 3 7 3.2377 - 3.0756 1.00 2911 177 0.2105 0.2631 REMARK 3 8 3.0756 - 2.9417 1.00 3008 118 0.2279 0.2887 REMARK 3 9 2.9417 - 2.8285 1.00 2882 184 0.2292 0.2935 REMARK 3 10 2.8285 - 2.7309 1.00 2936 165 0.2378 0.2602 REMARK 3 11 2.7309 - 2.6455 1.00 2879 153 0.2189 0.2301 REMARK 3 12 2.6455 - 2.5699 1.00 2964 171 0.2321 0.3137 REMARK 3 13 2.5699 - 2.5022 1.00 2925 146 0.2352 0.2767 REMARK 3 14 2.5022 - 2.4412 1.00 2938 184 0.2306 0.2977 REMARK 3 15 2.4412 - 2.3857 1.00 2941 143 0.2386 0.2741 REMARK 3 16 2.3857 - 2.3349 1.00 2913 119 0.2404 0.3408 REMARK 3 17 2.3349 - 2.2882 1.00 2962 140 0.2343 0.2584 REMARK 3 18 2.2882 - 2.2451 1.00 2904 163 0.2295 0.2502 REMARK 3 19 2.2451 - 2.2050 1.00 2990 153 0.2278 0.3141 REMARK 3 20 2.2050 - 2.1676 1.00 3001 129 0.2491 0.2715 REMARK 3 21 2.1676 - 2.1326 1.00 2902 155 0.2591 0.2972 REMARK 3 22 2.1326 - 2.0998 1.00 2935 133 0.2551 0.2740 REMARK 3 23 2.0998 - 2.0689 1.00 2931 142 0.2683 0.3150 REMARK 3 24 2.0689 - 2.0398 1.00 2984 140 0.2805 0.2808 REMARK 3 25 2.0398 - 2.0122 1.00 2921 163 0.3035 0.2899 REMARK 3 26 2.0122 - 1.9861 1.00 2958 154 0.3140 0.3946 REMARK 3 27 1.9861 - 1.9613 1.00 2854 183 0.3145 0.3428 REMARK 3 28 1.9613 - 1.9376 1.00 2950 156 0.3498 0.3602 REMARK 3 29 1.9376 - 1.9151 0.99 2838 166 0.3695 0.4127 REMARK 3 30 1.9151 - 1.8900 0.86 2559 119 0.4064 0.3906 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 40.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.250 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) : 1.15010 REMARK 3 B22 (A**2) : 1.15010 REMARK 3 B33 (A**2) : -2.30020 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 : 0.005 5198 REMARK 3 ANGLE : 0.628 7190 REMARK 3 CHIRALITY : 0.041 780 REMARK 3 PLANARITY : 0.003 853 REMARK 3 DIHEDRAL : 14.701 2062 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 293:452) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3981 -41.1208 -18.5918 REMARK 3 T TENSOR REMARK 3 T11: 0.1867 T22: 0.1380 REMARK 3 T33: 0.1432 T12: 0.0028 REMARK 3 T13: 0.0171 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.9799 L22: 2.1406 REMARK 3 L33: 1.1932 L12: -0.3228 REMARK 3 L13: -0.0352 L23: 0.4462 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: 0.0527 S13: -0.2063 REMARK 3 S21: -0.1078 S22: 0.0138 S23: -0.1893 REMARK 3 S31: 0.2527 S32: 0.1258 S33: -0.0019 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 453:603) REMARK 3 ORIGIN FOR THE GROUP (A): 35.4252 -10.8407 1.7706 REMARK 3 T TENSOR REMARK 3 T11: 0.1426 T22: 0.1057 REMARK 3 T33: 0.1723 T12: -0.0314 REMARK 3 T13: 0.0192 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.9519 L22: 1.3851 REMARK 3 L33: 1.1814 L12: 0.6227 REMARK 3 L13: 0.4867 L23: 0.5370 REMARK 3 S TENSOR REMARK 3 S11: 0.0442 S12: -0.1629 S13: 0.2157 REMARK 3 S21: 0.1316 S22: -0.0939 S23: 0.1162 REMARK 3 S31: -0.1447 S32: 0.0040 S33: 0.0466 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 604:685) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3008 -13.8795 -8.5307 REMARK 3 T TENSOR REMARK 3 T11: 0.3800 T22: 0.6104 REMARK 3 T33: 0.3447 T12: 0.2323 REMARK 3 T13: -0.0331 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 1.5775 L22: 0.8261 REMARK 3 L33: 3.0971 L12: 0.6702 REMARK 3 L13: -0.2476 L23: -1.2099 REMARK 3 S TENSOR REMARK 3 S11: -0.2085 S12: -0.7057 S13: 0.6561 REMARK 3 S21: 0.4823 S22: 0.2322 S23: 0.2377 REMARK 3 S31: -1.5060 S32: -0.9131 S33: -0.1321 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 686:832) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5160 -24.6616 -13.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.0867 T22: 0.1375 REMARK 3 T33: 0.0686 T12: 0.0000 REMARK 3 T13: -0.0181 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 1.1659 L22: 1.4470 REMARK 3 L33: 3.0719 L12: 0.3254 REMARK 3 L13: 0.0606 L23: -0.7760 REMARK 3 S TENSOR REMARK 3 S11: -0.1201 S12: 0.0750 S13: 0.0612 REMARK 3 S21: 0.0857 S22: 0.2306 S23: 0.1137 REMARK 3 S31: -0.1807 S32: -0.8386 S33: -0.0744 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 36.3316 -22.8892 4.1649 REMARK 3 T TENSOR REMARK 3 T11: 0.2441 T22: 0.1891 REMARK 3 T33: 0.2267 T12: -0.0784 REMARK 3 T13: -0.0344 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 6.1797 L22: 1.4448 REMARK 3 L33: 2.6306 L12: -0.7723 REMARK 3 L13: 2.3878 L23: -0.9759 REMARK 3 S TENSOR REMARK 3 S11: 0.1485 S12: -0.0165 S13: -0.4802 REMARK 3 S21: 0.3291 S22: -0.1833 S23: -0.1008 REMARK 3 S31: 0.0906 S32: 0.3415 S33: 0.0517 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' REMARK 3 ORIGIN FOR THE GROUP (A): 34.1943 -23.7012 5.5739 REMARK 3 T TENSOR REMARK 3 T11: 0.1920 T22: 0.1903 REMARK 3 T33: 0.0716 T12: -0.0310 REMARK 3 T13: -0.0004 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 3.2546 L22: 2.8567 REMARK 3 L33: 2.6293 L12: 0.6409 REMARK 3 L13: 2.2210 L23: 0.3692 REMARK 3 S TENSOR REMARK 3 S11: -0.0952 S12: -0.4525 S13: -0.0369 REMARK 3 S21: 0.3273 S22: 0.0404 S23: -0.1428 REMARK 3 S31: -0.0273 S32: -0.0586 S33: 0.0336 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 4DLG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070477. 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 : 6.5 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) : 1.23 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) 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 : 47964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.7.3_928 REMARK 200 STARTING MODEL: PDB ENTRY 3KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CACODYLATE, 0.2 M NH4(OAC), REMARK 280 10 MM MG(OAC)2, 15% PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 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 29.85133 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 59.70267 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 59.70267 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 29.85133 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: 7850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 906 LIES ON A SPECIAL POSITION. REMARK 375 OXT ACT A 906 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 DA C 201 REMARK 465 DA C 202 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 O2 GOL C 302 O HOH C 414 2.18 REMARK 500 OP2 DG B 110 O HOH B 224 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 ACT A 906 CH3 ACT A 906 5554 0.32 REMARK 500 C ACT A 906 O ACT A 906 5554 1.25 REMARK 500 C ACT A 906 CH3 ACT A 906 5554 1.50 REMARK 500 O ACT A 906 OXT ACT A 906 5554 2.16 REMARK 500 O ACT A 906 O ACT A 906 5554 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. = 1.8 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 203 O4' - C1' - N9 ANGL. DEV. = 2.3 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 321 95.66 -64.97 REMARK 500 ASP A 381 113.29 -162.22 REMARK 500 THR A 399 -162.31 -104.44 REMARK 500 VAL A 433 -71.60 -121.28 REMARK 500 TYR A 545 -59.91 -124.09 REMARK 500 VAL A 586 -16.41 -158.90 REMARK 500 LEU A 780 -62.39 -95.53 REMARK 500 HIS A 784 -66.76 65.17 REMARK 500 TYR A 811 84.54 -160.52 REMARK 500 LEU A 813 -166.41 -112.63 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 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 80.8 REMARK 620 3 ASP A 785 OD2 84.2 101.4 REMARK 620 4 DCT A 901 O2G 101.1 93.0 165.3 REMARK 620 5 DCT A 901 O2B 177.2 96.8 94.8 80.6 REMARK 620 6 DCT A 901 O2A 107.4 170.6 75.3 90.0 74.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 610 OD1 47.7 REMARK 620 3 ASP A 785 OD1 119.1 83.3 REMARK 620 4 DCT A 901 O2A 108.1 80.5 93.1 REMARK 620 5 HOH A1053 O 87.6 127.4 149.3 92.1 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 DCT 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 MG 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 GOL A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB DBREF 4DLG A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4DLG C 201 216 PDB 4DLG 4DLG 201 216 DBREF 4DLG B 101 112 PDB 4DLG 4DLG 101 112 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 DG DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4DLG DOC B 112 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HET DOC B 112 18 HET DCT A 901 27 HET MG A 902 1 HET MG A 903 1 HET ACT A 904 4 HET ACT A 905 4 HET ACT A 906 4 HET GOL A 907 6 HET GOL C 301 6 HET GOL C 302 6 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 4 DCT C9 H16 N3 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 10 GOL 3(C3 H8 O3) FORMUL 13 HOH *445(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 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 PHE A 647 1 11 HELIX 18 18 PRO A 650 VAL A 654 5 5 HELIX 19 19 ASP A 655 ALA A 662 1 8 HELIX 20 20 ALA A 662 TYR A 671 1 10 HELIX 21 21 SER A 674 LEU A 682 1 9 HELIX 22 22 PRO A 685 SER A 699 1 15 HELIX 23 23 PHE A 700 GLY A 718 1 19 HELIX 24 24 PRO A 731 ALA A 735 5 5 HELIX 25 25 VAL A 737 GLU A 774 1 38 HELIX 26 26 ARG A 795 GLY A 809 1 15 HELIX 27 27 LEU A 828 GLU A 832 5 5 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 ALA A 297 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 GLU A 820 N ASP A 610 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 DOC B 112 1555 1555 1.60 LINK OD1 ASP A 610 MG MG A 902 1555 1555 1.99 LINK OD2 ASP A 610 MG MG A 903 1555 1555 2.15 LINK OD1 ASP A 610 MG MG A 903 1555 1555 2.95 LINK O TYR A 611 MG MG A 902 1555 1555 1.93 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.06 LINK OD1 ASP A 785 MG MG A 903 1555 1555 2.16 LINK O2G DCT A 901 MG MG A 902 1555 1555 1.91 LINK O2B DCT A 901 MG MG A 902 1555 1555 2.06 LINK O2A DCT A 901 MG MG A 902 1555 1555 2.25 LINK O2A DCT A 901 MG MG A 903 1555 1555 2.28 LINK MG MG A 903 O HOH A1053 1555 1555 2.08 CISPEP 1 TRP A 299 PRO A 300 0 1.13 CISPEP 2 ASP A 578 PRO A 579 0 -4.77 SITE 1 AC1 21 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC1 21 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC1 21 ARG A 659 LYS A 663 PHE A 667 ASP A 785 SITE 4 AC1 21 MG A 902 MG A 903 HOH A1053 HOH A1219 SITE 5 AC1 21 HOH A1221 HOH A1233 DOC B 112 DG C 204 SITE 6 AC1 21 DG C 205 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 DCT A 901 SITE 2 AC2 5 MG A 903 SITE 1 AC3 7 ASP A 610 ASP A 785 GLU A 786 DCT A 901 SITE 2 AC3 7 MG A 902 HOH A1053 DOC B 112 SITE 1 AC4 5 PHE A 309 LEU A 311 ARG A 405 HOH A1099 SITE 2 AC4 5 HOH A1358 SITE 1 AC5 3 TRP A 417 ARG A 431 ARG A 435 SITE 1 AC6 2 TYR A 455 HOH A1203 SITE 1 AC7 11 ASN A 485 SER A 486 ARG A 487 ASP A 488 SITE 2 AC7 11 HOH A1043 HOH A1368 DC B 106 HOH B 228 SITE 3 AC7 11 DG C 211 DT C 212 HOH C 404 SITE 1 AC8 6 DA B 102 DC B 103 DG C 213 DG C 214 SITE 2 AC8 6 DT C 215 HOH C 438 SITE 1 AC9 8 ASP A 578 PRO A 579 DC C 209 DC C 210 SITE 2 AC9 8 HOH C 414 HOH C 427 HOH C 431 HOH C 442 CRYST1 107.784 107.784 89.554 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 0.009278 0.005357 0.000000 0.00000 SCALE2 0.000000 0.010713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011166 0.00000