HEADER TRANSFERASE 31-MAR-17 5NKL TITLE CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM TITLE 2 THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH THE ARTIFICIAL TITLE 3 BASE PAIR DDS-DPXTP 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*(DNU) COMPND 13 P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-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 DNA POLYMERASE, ARTIFICIAL BASE PAIR, UNNATURAL BASE PAIR, TERNARY KEYWDS 2 COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,A.MARX,K.DIEDERICHS,I.HIRAO,M.KIMOTO REVDAT 3 27-SEP-17 5NKL 1 JRNL REVDAT 2 05-JUL-17 5NKL 1 JRNL REVDAT 1 28-JUN-17 5NKL 0 JRNL AUTH K.BETZ,M.KIMOTO,K.DIEDERICHS,I.HIRAO,A.MARX JRNL TITL STRUCTURAL BASIS FOR EXPANSION OF THE GENETIC ALPHABET WITH JRNL TITL 2 AN ARTIFICIAL NUCLEOBASE PAIR. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 12000 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28594080 JRNL DOI 10.1002/ANIE.201704190 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2650: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 129943 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 6580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.1199 - 5.2800 1.00 4165 240 0.1399 0.1831 REMARK 3 2 5.2800 - 4.1917 1.00 4150 206 0.1132 0.1850 REMARK 3 3 4.1917 - 3.6621 1.00 4151 259 0.1291 0.1790 REMARK 3 4 3.6621 - 3.3274 1.00 4153 229 0.1449 0.1928 REMARK 3 5 3.3274 - 3.0889 1.00 4114 257 0.1722 0.2301 REMARK 3 6 3.0889 - 2.9068 0.99 4165 211 0.1892 0.3007 REMARK 3 7 2.9068 - 2.7613 1.00 4149 229 0.2017 0.2509 REMARK 3 8 2.7613 - 2.6411 0.99 4119 215 0.1859 0.2657 REMARK 3 9 2.6411 - 2.5394 0.99 4134 229 0.1755 0.2334 REMARK 3 10 2.5394 - 2.4518 0.99 4143 246 0.1851 0.2604 REMARK 3 11 2.4518 - 2.3751 0.99 4127 195 0.1918 0.2445 REMARK 3 12 2.3751 - 2.3072 0.99 4201 174 0.1995 0.2687 REMARK 3 13 2.3072 - 2.2465 0.99 4071 242 0.2018 0.2485 REMARK 3 14 2.2465 - 2.1917 0.99 4217 178 0.2138 0.2893 REMARK 3 15 2.1917 - 2.1419 0.99 4065 205 0.2154 0.2544 REMARK 3 16 2.1419 - 2.0963 0.99 4143 191 0.2286 0.2694 REMARK 3 17 2.0963 - 2.0544 0.99 4087 214 0.2409 0.2945 REMARK 3 18 2.0544 - 2.0156 0.98 4135 230 0.2647 0.2877 REMARK 3 19 2.0156 - 1.9796 0.98 4061 230 0.2757 0.3314 REMARK 3 20 1.9796 - 1.9460 0.98 4081 233 0.2822 0.3203 REMARK 3 21 1.9460 - 1.9146 0.98 4133 200 0.2902 0.3568 REMARK 3 22 1.9146 - 1.8852 0.98 4028 235 0.3226 0.3693 REMARK 3 23 1.8852 - 1.8575 0.98 4152 199 0.3115 0.3401 REMARK 3 24 1.8575 - 1.8313 0.98 4062 245 0.3248 0.3772 REMARK 3 25 1.8313 - 1.8065 0.98 4038 225 0.3417 0.3654 REMARK 3 26 1.8065 - 1.7831 0.98 4090 201 0.3415 0.3615 REMARK 3 27 1.7831 - 1.7608 0.97 4086 226 0.3759 0.4072 REMARK 3 28 1.7608 - 1.7396 0.98 4112 205 0.3735 0.4306 REMARK 3 29 1.7396 - 1.7193 0.97 4026 221 0.3831 0.4084 REMARK 3 30 1.7193 - 1.7000 0.97 4005 210 0.3856 0.4384 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.900 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 : 0.011 5141 REMARK 3 ANGLE : 1.198 7085 REMARK 3 CHIRALITY : 0.062 771 REMARK 3 PLANARITY : 0.009 848 REMARK 3 DIHEDRAL : 18.078 3030 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 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3040 -41.0432 -18.2932 REMARK 3 T TENSOR REMARK 3 T11: 0.3247 T22: 0.2400 REMARK 3 T33: 0.3405 T12: -0.1327 REMARK 3 T13: 0.0709 T23: -0.0289 REMARK 3 L TENSOR REMARK 3 L11: 0.2866 L22: 0.5408 REMARK 3 L33: 0.6778 L12: -0.0255 REMARK 3 L13: 0.1417 L23: 0.5384 REMARK 3 S TENSOR REMARK 3 S11: 0.0270 S12: 0.0645 S13: -0.1209 REMARK 3 S21: -0.1749 S22: 0.0288 S23: -0.1689 REMARK 3 S31: 0.1257 S32: -0.0256 S33: 0.0027 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.9257 -11.0050 1.7279 REMARK 3 T TENSOR REMARK 3 T11: 0.3278 T22: 0.1756 REMARK 3 T33: 0.2759 T12: -0.0758 REMARK 3 T13: 0.0320 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.9035 L22: 0.7643 REMARK 3 L33: 0.6428 L12: 0.5834 REMARK 3 L13: -0.4845 L23: -0.3865 REMARK 3 S TENSOR REMARK 3 S11: 0.0421 S12: -0.0007 S13: 0.1452 REMARK 3 S21: 0.0316 S22: 0.0123 S23: 0.1416 REMARK 3 S31: -0.2817 S32: -0.0016 S33: 0.0015 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 604 THROUGH 685 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8072 -13.6388 -8.5115 REMARK 3 T TENSOR REMARK 3 T11: 0.3807 T22: 0.6203 REMARK 3 T33: 0.2721 T12: 0.0897 REMARK 3 T13: -0.0402 T23: 0.0923 REMARK 3 L TENSOR REMARK 3 L11: 0.0148 L22: 0.4768 REMARK 3 L33: 0.1156 L12: -0.0793 REMARK 3 L13: -0.0194 L23: 0.1081 REMARK 3 S TENSOR REMARK 3 S11: -0.1317 S12: -0.0963 S13: 0.0822 REMARK 3 S21: -0.0319 S22: 0.1812 S23: 0.0646 REMARK 3 S31: -0.3397 S32: -0.3267 S33: 0.0106 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 686 THROUGH 831 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.4303 -24.9390 -13.3223 REMARK 3 T TENSOR REMARK 3 T11: 0.2667 T22: 0.4714 REMARK 3 T33: 0.2355 T12: -0.0822 REMARK 3 T13: -0.0174 T23: 0.0510 REMARK 3 L TENSOR REMARK 3 L11: 0.3540 L22: 0.5465 REMARK 3 L33: 1.2917 L12: -0.1154 REMARK 3 L13: 0.1902 L23: -0.2939 REMARK 3 S TENSOR REMARK 3 S11: -0.1379 S12: 0.0410 S13: -0.0564 REMARK 3 S21: -0.1789 S22: 0.1788 S23: 0.0151 REMARK 3 S31: -0.1835 S32: -0.5432 S33: -0.0280 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.9716 -23.3841 5.3146 REMARK 3 T TENSOR REMARK 3 T11: 0.2074 T22: 0.3289 REMARK 3 T33: 0.3199 T12: -0.0096 REMARK 3 T13: 0.0041 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 0.0738 L22: 0.1130 REMARK 3 L33: 0.2456 L12: 0.1198 REMARK 3 L13: -0.1799 L23: -0.1059 REMARK 3 S TENSOR REMARK 3 S11: 0.0248 S12: 0.1193 S13: 0.0230 REMARK 3 S21: 0.2015 S22: -0.0953 S23: 0.1297 REMARK 3 S31: -0.3095 S32: 0.4453 S33: -0.0323 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.5103 -22.8961 6.3047 REMARK 3 T TENSOR REMARK 3 T11: 0.2656 T22: 0.3398 REMARK 3 T33: 0.2767 T12: -0.0217 REMARK 3 T13: -0.0094 T23: 0.0477 REMARK 3 L TENSOR REMARK 3 L11: 0.0182 L22: 0.3817 REMARK 3 L33: 0.5283 L12: 0.1217 REMARK 3 L13: -0.1119 L23: 0.4359 REMARK 3 S TENSOR REMARK 3 S11: -0.2548 S12: -0.0886 S13: -0.1626 REMARK 3 S21: 0.0158 S22: 0.1941 S23: -0.0655 REMARK 3 S31: -0.0790 S32: -0.1235 S33: -0.0010 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 5NKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-16 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) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 130009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.113 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3RTV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 8.5, 0.2M SODIUM REMARK 280 ACETATE, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 30.19033 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 60.38067 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 60.38067 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 30.19033 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: 7010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 HOH A1231 LIES ON A SPECIAL POSITION. 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 HE ARG A 431 O HOH A 1002 1.42 REMARK 500 HE ARG A 716 O HOH A 1003 1.43 REMARK 500 MG MG A 902 H20 91R A 905 1.60 REMARK 500 O HOH A 1212 O HOH C 429 1.91 REMARK 500 OD2 ASP A 625 O HOH A 1001 1.94 REMARK 500 O HOH A 1089 O HOH A 1198 2.02 REMARK 500 O HOH A 1115 O HOH A 1198 2.06 REMARK 500 O HOH A 1027 O HOH A 1189 2.10 REMARK 500 O HOH A 1204 O HOH A 1227 2.12 REMARK 500 O HOH A 1115 O HOH C 426 2.16 REMARK 500 O HOH B 205 O HOH B 222 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA B 102 O3' DA B 102 C3' -0.041 REMARK 500 DG B 108 O3' DG B 108 C3' -0.038 REMARK 500 DC B 109 N3 DC B 109 C4 -0.049 REMARK 500 DG C 205 P DG C 205 O5' 0.061 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 101 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 110 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 210 OP1 - P - OP2 ANGL. DEV. = 11.2 DEGREES REMARK 500 DC C 210 O5' - P - OP1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT C 212 O5' - P - OP2 ANGL. DEV. = -7.2 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 215 O4' - C1' - N1 ANGL. DEV. = 1.9 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 ASP A 381 106.09 -162.31 REMARK 500 THR A 399 -164.98 -104.94 REMARK 500 VAL A 433 -71.53 -121.78 REMARK 500 ASP A 496 -61.25 -94.41 REMARK 500 ILE A 503 -67.71 -96.44 REMARK 500 HIS A 526 136.63 -175.38 REMARK 500 TYR A 545 -56.37 -129.62 REMARK 500 VAL A 586 -23.65 -161.67 REMARK 500 ALA A 683 72.08 57.25 REMARK 500 HIS A 784 -57.13 68.78 REMARK 500 TYR A 811 94.15 -170.48 REMARK 500 LYS A 831 48.00 -106.18 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 85.7 REMARK 620 3 ASP A 785 OD2 88.0 84.9 REMARK 620 4 91T A 904 O6 102.9 169.3 89.0 REMARK 620 5 91T A 904 O9 175.2 90.0 89.5 81.1 REMARK 620 6 91R A 905 O6 102.5 166.4 84.6 4.4 81.4 REMARK 620 7 91R A 905 O9 172.9 87.9 88.4 83.1 2.3 83.3 REMARK 620 8 91T A 904 O13 89.2 98.4 175.6 88.3 93.4 92.7 94.7 REMARK 620 9 91R A 905 O14 92.2 96.7 178.4 89.5 90.4 93.8 91.6 3.5 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 110.3 REMARK 620 3 91T A 904 O6 103.8 92.5 REMARK 620 4 91R A 905 O6 106.2 89.1 3.6 REMARK 620 5 HOH A1006 O 88.3 93.3 163.7 163.4 REMARK 620 6 HOH A1168 O 88.3 161.4 83.4 86.3 86.2 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 ACT A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 91T A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 91R A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 302 DBREF 5NKL A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5NKL B 101 112 PDB 5NKL 5NKL 101 112 DBREF 5NKL C 201 216 PDB 5NKL 5NKL 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 91N DG DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET DOC B 112 30 HET 91N C 204 38 HET MG A 901 1 HET MG A 902 1 HET ACT A 903 7 HET 91T A 904 56 HET 91R A 905 56 HET GOL C 301 14 HET GOL C 302 14 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 91N [(2~{R},3~{S},5~{R})-3-OXIDANYL-5-(7-THIOPHEN-2- HETNAM 2 91N YLIMIDAZO[4,5-B]PYRIDIN-3-YL)OXOLAN-2-YL]METHYL HETNAM 3 91N DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM 91T [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-BIS(OXIDANYL) HETNAM 2 91T PENT-1-YNYL]-2-NITRO-PYRROL-1-YL]-3-OXIDANYL-OXOLAN-2- HETNAM 3 91T YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN HETNAM 4 91T PHOSPHATE HETNAM 91R [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-BIS(OXIDANYL) HETNAM 2 91R PENT-1-YNYL]-2-NITRO-PYRROL-1-YL]-3-OXIDANYL-OXOLAN-2- HETNAM 3 91R YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN HETNAM 4 91R PHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 91N C15 H16 N3 O6 P S FORMUL 4 MG 2(MG 2+) FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 91T C14 H21 N2 O16 P3 FORMUL 8 91R C14 H21 N2 O16 P3 FORMUL 9 GOL 2(C3 H8 O3) FORMUL 11 HOH *303(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 ALA A 521 1 7 HELIX 11 AB2 HIS A 526 TYR A 545 1 20 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 PHE A 306 O ALA A 327 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 577 N ARG A 563 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 OD1 ASP A 610 MG MG A 902 1555 1555 1.99 LINK OD2 ASP A 610 MG MG A 901 1555 1555 2.32 LINK O TYR A 611 MG MG A 902 1555 1555 2.13 LINK OD1 ASP A 785 MG MG A 901 1555 1555 2.21 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.06 LINK O3' DC B 111 P DOC B 112 1555 1555 1.56 LINK O3' DA C 203 P 91N C 204 1555 1555 1.61 LINK O3' 91N C 204 P DG C 205 1555 1555 1.60 LINK MG MG A 901 O6 A91T A 904 1555 1555 2.34 LINK MG MG A 901 O6 B91R A 905 1555 1555 2.26 LINK MG MG A 901 O HOH A1006 1555 1555 2.37 LINK MG MG A 901 O HOH A1168 1555 1555 2.56 LINK MG MG A 902 O6 A91T A 904 1555 1555 2.19 LINK MG MG A 902 O9 A91T A 904 1555 1555 2.24 LINK MG MG A 902 O6 B91R A 905 1555 1555 2.20 LINK MG MG A 902 O9 B91R A 905 1555 1555 2.22 LINK MG MG A 902 O13A91T A 904 1555 1555 2.08 LINK MG MG A 902 O14B91R A 905 1555 1555 1.97 CISPEP 1 TRP A 299 PRO A 300 0 4.80 CISPEP 2 ASP A 578 PRO A 579 0 1.29 SITE 1 AC1 7 ASP A 610 ASP A 785 MG A 902 91T A 904 SITE 2 AC1 7 91R A 905 HOH A1006 HOH A1168 SITE 1 AC2 6 ASP A 610 TYR A 611 ASP A 785 MG A 901 SITE 2 AC2 6 91T A 904 91R A 905 SITE 1 AC3 2 PHE A 724 HOH A1043 SITE 1 AC4 26 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC4 26 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC4 26 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC4 26 TYR A 671 ASP A 785 MG A 901 MG A 902 SITE 5 AC4 26 91R A 905 HOH A1007 HOH A1025 HOH A1054 SITE 6 AC4 26 HOH A1056 HOH A1168 DOC B 112 HOH B 208 SITE 7 AC4 26 91N C 204 DG C 205 SITE 1 AC5 26 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC5 26 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC5 26 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC5 26 TYR A 671 ASP A 785 MG A 901 MG A 902 SITE 5 AC5 26 91T A 904 HOH A1007 HOH A1025 HOH A1054 SITE 6 AC5 26 HOH A1056 HOH A1168 DOC B 112 HOH B 208 SITE 7 AC5 26 91N C 204 DG C 205 SITE 1 AC6 5 DC B 111 HOH B 206 DG C 205 DG C 206 SITE 2 AC6 5 GOL C 302 SITE 1 AC7 5 DG C 205 DG C 206 GOL C 301 HOH C 406 SITE 2 AC7 5 HOH C 409 CRYST1 108.777 108.777 90.571 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 0.009193 0.005308 0.000000 0.00000 SCALE2 0.000000 0.010615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011041 0.00000 MASTER 484 0 9 25 14 0 23 6 0 0 0 45 END