HEADER TRANSFERASE/DNA 16-FEB-12 4DQS TITLE BINARY COMPLEX OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT AND DUPLEX TITLE 2 DNA WITH RC IN PRIMER TERMINUS PAIRED WITH DG OF TEMPLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UN RESIDUES 287-878; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA TEMPLATE STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 STRAIN: HTA426; SOURCE 5 GENE: POLA, GK2730; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DNA POLYMERASE I, PROTEIN-DNA COMPLEX, RC-DG, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.WANG,L.S.BEESE REVDAT 3 21-NOV-12 4DQS 1 JRNL REVDAT 2 13-JUN-12 4DQS 1 JRNL REVDAT 1 06-JUN-12 4DQS 0 JRNL AUTH W.WANG,E.Y.WU,H.W.HELLINGA,L.S.BEESE JRNL TITL STRUCTURAL FACTORS THAT DETERMINE SELECTIVITY OF A HIGH JRNL TITL 2 FIDELITY DNA POLYMERASE FOR DEOXY-, DIDEOXY-, AND JRNL TITL 3 RIBONUCLEOTIDES. JRNL REF J.BIOL.CHEM. V. 287 28215 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22648417 JRNL DOI 10.1074/JBC.M112.366609 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.WANG,H.W.HELLINGA,L.S.BEESE REMARK 1 TITL STRUCTURAL EVIDENCE FOR THE RARE TAUTOMER HYPOTHESIS OF REMARK 1 TITL 2 SPONTANEOUS MUTAGENESIS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 108 17644 2011 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1026) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 103589 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 5031 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 45.3987 - 5.1556 0.98 3438 195 0.1901 0.1940 REMARK 3 2 5.1556 - 4.0930 1.00 3414 164 0.1331 0.1393 REMARK 3 3 4.0930 - 3.5759 1.00 3344 168 0.1374 0.1493 REMARK 3 4 3.5759 - 3.2490 1.00 3329 189 0.1430 0.1772 REMARK 3 5 3.2490 - 3.0162 1.00 3320 151 0.1625 0.1883 REMARK 3 6 3.0162 - 2.8384 1.00 3329 163 0.1579 0.1852 REMARK 3 7 2.8384 - 2.6963 1.00 3276 188 0.1555 0.1678 REMARK 3 8 2.6963 - 2.5789 1.00 3301 162 0.1565 0.1847 REMARK 3 9 2.5789 - 2.4796 1.00 3303 173 0.1457 0.1839 REMARK 3 10 2.4796 - 2.3941 1.00 3270 184 0.1434 0.1746 REMARK 3 11 2.3941 - 2.3192 1.00 3285 174 0.1456 0.1436 REMARK 3 12 2.3192 - 2.2529 0.99 3213 190 0.1487 0.1705 REMARK 3 13 2.2529 - 2.1936 0.99 3244 163 0.1653 0.1867 REMARK 3 14 2.1936 - 2.1401 1.00 3276 170 0.1493 0.1807 REMARK 3 15 2.1401 - 2.0915 1.00 3290 170 0.1497 0.1686 REMARK 3 16 2.0915 - 2.0469 1.00 3267 149 0.1548 0.1781 REMARK 3 17 2.0469 - 2.0060 1.00 3312 136 0.1564 0.1756 REMARK 3 18 2.0060 - 1.9681 1.00 3302 128 0.1736 0.1790 REMARK 3 19 1.9681 - 1.9330 1.00 3279 132 0.1731 0.1943 REMARK 3 20 1.9330 - 1.9002 0.99 3281 172 0.2230 0.2879 REMARK 3 21 1.9002 - 1.8696 1.00 3222 170 0.1886 0.2480 REMARK 3 22 1.8696 - 1.8408 1.00 3261 172 0.1850 0.2094 REMARK 3 23 1.8408 - 1.8137 1.00 3241 170 0.1821 0.2291 REMARK 3 24 1.8137 - 1.7882 1.00 3258 172 0.1885 0.2301 REMARK 3 25 1.7882 - 1.7640 1.00 3258 171 0.1935 0.2193 REMARK 3 26 1.7640 - 1.7411 1.00 3272 172 0.1953 0.2038 REMARK 3 27 1.7411 - 1.7193 1.00 3243 171 0.2071 0.2304 REMARK 3 28 1.7193 - 1.6986 1.00 3220 169 0.2139 0.2270 REMARK 3 29 1.6986 - 1.6789 1.00 3258 172 0.2301 0.2412 REMARK 3 30 1.6789 - 1.6600 1.00 3252 171 0.2466 0.2572 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.20360 REMARK 3 B22 (A**2) : -3.15480 REMARK 3 B33 (A**2) : -2.04880 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 : 0.010 5336 REMARK 3 ANGLE : 1.291 7338 REMARK 3 CHIRALITY : 0.071 826 REMARK 3 PLANARITY : 0.006 871 REMARK 3 DIHEDRAL : 16.330 2074 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain 'A' and (resseq 298:467) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5438 25.9020 5.8720 REMARK 3 T TENSOR REMARK 3 T11: 0.1298 T22: 0.1456 REMARK 3 T33: 0.1144 T12: -0.0054 REMARK 3 T13: 0.0161 T23: -0.0163 REMARK 3 L TENSOR REMARK 3 L11: 1.6916 L22: 1.5344 REMARK 3 L33: 1.0240 L12: 0.6817 REMARK 3 L13: -0.4587 L23: 0.0100 REMARK 3 S TENSOR REMARK 3 S11: -0.0906 S12: 0.2526 S13: -0.1469 REMARK 3 S21: -0.2148 S22: 0.0482 S23: -0.0784 REMARK 3 S31: 0.1077 S32: -0.0399 S33: 0.0257 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain 'A' and (resseq 468:522) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9971 43.4717 25.1647 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.2327 REMARK 3 T33: 0.1111 T12: -0.0262 REMARK 3 T13: -0.0043 T23: 0.0442 REMARK 3 L TENSOR REMARK 3 L11: 0.3472 L22: 1.0864 REMARK 3 L33: 1.3405 L12: -0.2585 REMARK 3 L13: -0.4996 L23: -0.3219 REMARK 3 S TENSOR REMARK 3 S11: 0.0151 S12: -0.2389 S13: 0.1954 REMARK 3 S21: 0.1166 S22: -0.1375 S23: -0.1999 REMARK 3 S31: -0.1001 S32: 0.4285 S33: 0.0618 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain 'A' and (resseq 523:604) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1207 37.7457 39.4699 REMARK 3 T TENSOR REMARK 3 T11: 0.5029 T22: 0.4227 REMARK 3 T33: 0.2604 T12: 0.1370 REMARK 3 T13: -0.0526 T23: 0.0311 REMARK 3 L TENSOR REMARK 3 L11: 0.5001 L22: 1.0756 REMARK 3 L33: 2.0928 L12: -0.5698 REMARK 3 L13: 1.3303 L23: -0.0367 REMARK 3 S TENSOR REMARK 3 S11: 0.0681 S12: 0.0771 S13: 0.0312 REMARK 3 S21: 0.4675 S22: 0.1016 S23: -0.1042 REMARK 3 S31: 0.7291 S32: 0.6300 S33: -0.0405 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain 'A' and (resseq 605:876) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9236 44.5852 35.9732 REMARK 3 T TENSOR REMARK 3 T11: 0.1116 T22: 0.1165 REMARK 3 T33: 0.1354 T12: -0.0138 REMARK 3 T13: -0.0054 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.5975 L22: 0.7195 REMARK 3 L33: 0.6515 L12: -0.0339 REMARK 3 L13: -0.0493 L23: 0.0734 REMARK 3 S TENSOR REMARK 3 S11: 0.0269 S12: -0.0669 S13: 0.0140 REMARK 3 S21: 0.1079 S22: -0.0267 S23: -0.0771 REMARK 3 S31: 0.0378 S32: 0.0169 S33: 0.0050 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: chain 'B' and (resseq 18:22) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0657 20.3172 25.8000 REMARK 3 T TENSOR REMARK 3 T11: 1.5614 T22: 0.9026 REMARK 3 T33: 1.0534 T12: 0.3906 REMARK 3 T13: 0.0767 T23: -0.3590 REMARK 3 L TENSOR REMARK 3 L11: 5.6544 L22: 6.9064 REMARK 3 L33: 5.7040 L12: -1.1539 REMARK 3 L13: 2.1992 L23: 2.0260 REMARK 3 S TENSOR REMARK 3 S11: 0.0185 S12: 0.9779 S13: -0.0946 REMARK 3 S21: -0.6227 S22: -0.0299 S23: -0.2613 REMARK 3 S31: 0.2953 S32: -0.1820 S33: 0.1876 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: chain 'B' and (resseq 23:29) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3843 35.7362 36.9031 REMARK 3 T TENSOR REMARK 3 T11: 0.3953 T22: 0.2848 REMARK 3 T33: 0.2286 T12: 0.0328 REMARK 3 T13: -0.0231 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 6.6924 L22: 5.3789 REMARK 3 L33: 3.5724 L12: -2.7718 REMARK 3 L13: 1.0902 L23: -0.5692 REMARK 3 S TENSOR REMARK 3 S11: -0.0634 S12: 0.0228 S13: -0.3929 REMARK 3 S21: 0.5510 S22: 0.0055 S23: -0.1543 REMARK 3 S31: 0.7003 S32: 0.3948 S33: 0.1204 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: chain 'C' and (resseq 3:10) REMARK 3 ORIGIN FOR THE GROUP (A): 21.5789 33.5134 33.4713 REMARK 3 T TENSOR REMARK 3 T11: 0.2971 T22: 0.3022 REMARK 3 T33: 0.2542 T12: 0.0443 REMARK 3 T13: -0.0348 T23: 0.0594 REMARK 3 L TENSOR REMARK 3 L11: 1.5938 L22: 2.2495 REMARK 3 L33: 0.9801 L12: -0.3422 REMARK 3 L13: 0.8595 L23: 0.8692 REMARK 3 S TENSOR REMARK 3 S11: -0.1619 S12: -0.2686 S13: 0.0083 REMARK 3 S21: 0.4490 S22: 0.0673 S23: -0.3136 REMARK 3 S31: 0.5474 S32: 0.4123 S33: 0.1289 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: chain 'C' and (resseq 11:16) REMARK 3 ORIGIN FOR THE GROUP (A): 36.5798 21.1057 33.2135 REMARK 3 T TENSOR REMARK 3 T11: 1.6083 T22: 0.4955 REMARK 3 T33: 0.7147 T12: 0.8321 REMARK 3 T13: -0.2919 T23: -0.2491 REMARK 3 L TENSOR REMARK 3 L11: 5.0173 L22: 3.2667 REMARK 3 L33: 2.0706 L12: -2.0482 REMARK 3 L13: -1.8409 L23: 1.8680 REMARK 3 S TENSOR REMARK 3 S11: -0.2146 S12: -0.0193 S13: -1.4181 REMARK 3 S21: 0.4520 S22: 0.0041 S23: 0.2891 REMARK 3 S31: 1.0894 S32: 0.2050 S33: -0.0572 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 4DQS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB070666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1158 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103591 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.340 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: PDB ENTRY 1L5U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 44%-49% SATURATED AMMONIUM SULFATE, REMARK 280 2.5% MPD, 10MM MNSO4, 100MM MES (PH 5.8), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 44.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.88000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.88000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 5460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 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 MET A 285 REMARK 465 GLU A 286 REMARK 465 SER A 287 REMARK 465 PRO A 288 REMARK 465 SER A 289 REMARK 465 SER A 290 REMARK 465 GLU A 291 REMARK 465 GLU A 292 REMARK 465 GLU A 293 REMARK 465 LYS A 294 REMARK 465 PRO A 295 REMARK 465 LEU A 296 REMARK 465 ALA A 297 REMARK 465 LYS A 548 REMARK 465 LYS A 549 REMARK 465 THR A 550 REMARK 465 LYS A 551 REMARK 465 THR A 552 REMARK 465 GLY A 553 REMARK 465 DG B 18 REMARK 465 DG C 1 REMARK 465 DA C 2 REMARK 465 DC C 15 REMARK 465 DA C 16 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 DC C 3 P OP1 OP2 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 HG CYS A 845 O HOH A 1488 1.28 REMARK 500 O HOH A 1689 O HOH A 1691 1.88 REMARK 500 SG CYS A 388 O HOH A 1725 1.93 REMARK 500 O HOH A 1517 O HOH A 1538 1.95 REMARK 500 O PRO A 531 O HOH A 1421 1.96 REMARK 500 O HOH C 127 O HOH C 137 1.97 REMARK 500 O HOH A 1729 O HOH A 1730 2.01 REMARK 500 O HOH A 1563 O HOH A 1592 2.04 REMARK 500 O HOH A 1322 O HOH A 1635 2.06 REMARK 500 O HOH A 1755 O HOH A 1760 2.06 REMARK 500 NH1 ARG A 435 O HOH A 1732 2.07 REMARK 500 O HOH A 1415 O HOH A 1731 2.08 REMARK 500 O HOH A 1504 O HOH A 1534 2.08 REMARK 500 SG CYS A 845 O HOH A 1488 2.08 REMARK 500 OE1 GLU A 309 O HOH A 1585 2.09 REMARK 500 O HOH A 1641 O HOH B 123 2.09 REMARK 500 OD1 ASP A 408 O HOH A 1726 2.10 REMARK 500 O HOH A 1514 O HOH A 1590 2.10 REMARK 500 O HOH A 1765 O HOH A 1769 2.10 REMARK 500 O HOH A 1643 O HOH A 1758 2.11 REMARK 500 O HOH A 1472 O HOH A 1487 2.11 REMARK 500 OH TYR A 577 O HOH A 1762 2.13 REMARK 500 O HOH A 1266 O HOH A 1326 2.14 REMARK 500 O HOH A 1636 O HOH A 1722 2.14 REMARK 500 O HOH A 1286 O HOH A 1640 2.14 REMARK 500 O HOH A 1694 O HOH A 1696 2.15 REMARK 500 O HOH A 1766 O HOH A 1771 2.15 REMARK 500 O HOH A 1723 O HOH A 1745 2.15 REMARK 500 O2 SO4 A 902 O HOH A 1764 2.15 REMARK 500 OH TYR A 714 O HOH A 1269 2.15 REMARK 500 N LYS A 298 O HOH A 1710 2.16 REMARK 500 O HOH A 1311 O HOH A 1482 2.16 REMARK 500 O HOH A 1429 O HOH A 1661 2.17 REMARK 500 O HOH A 1158 O HOH A 1753 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 1165 O HOH A 1226 3545 1.93 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 ARG A 859 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG C 4 O3' - P - OP2 ANGL. DEV. = 9.6 DEGREES REMARK 500 DA C 6 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG C 14 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 ASP A 402 94.91 -168.01 REMARK 500 ALA A 421 41.38 -88.55 REMARK 500 ILE A 588 -71.77 -104.05 REMARK 500 LEU A 610 -50.89 -123.00 REMARK 500 ILE A 628 -30.16 -146.01 REMARK 500 HIS A 768 23.46 80.42 REMARK 500 HIS A 829 -53.14 74.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTP A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DQP RELATED DB: PDB REMARK 900 RELATED ID: 4DQQ RELATED DB: PDB REMARK 900 RELATED ID: 4DQR RELATED DB: PDB REMARK 900 RELATED ID: 4DS4 RELATED DB: PDB REMARK 900 RELATED ID: 4DS5 RELATED DB: PDB REMARK 900 RELATED ID: 4DSE RELATED DB: PDB REMARK 900 RELATED ID: 4DSF RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF REMARK 999 GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT REMARK 999 DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE. DBREF 4DQS A 285 876 UNP Q5KWC1 Q5KWC1_GEOKA 287 878 DBREF 4DQS B 18 29 PDB 4DQS 4DQS 18 29 DBREF 4DQS C 1 16 PDB 4DQS 4DQS 1 16 SEQADV 4DQS HIS A 823 UNP Q5KWC1 ARG 825 SEE REMARK 999 SEQRES 1 A 592 MET GLU SER PRO SER SER GLU GLU GLU LYS PRO LEU ALA SEQRES 2 A 592 LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU GLU SEQRES 3 A 592 MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL VAL SEQRES 4 A 592 GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE ALA SEQRES 5 A 592 VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO GLU SEQRES 6 A 592 THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU GLY SEQRES 7 A 592 ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS ARG SEQRES 8 A 592 ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU CYS SEQRES 9 A 592 GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU LEU SEQRES 10 A 592 ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA ALA SEQRES 11 A 592 LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU ALA SEQRES 12 A 592 VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP GLU SEQRES 13 A 592 PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA ALA SEQRES 14 A 592 ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU ARG SEQRES 15 A 592 ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU GLN SEQRES 16 A 592 PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA GLY SEQRES 17 A 592 VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY LYS SEQRES 18 A 592 GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG ILE SEQRES 19 A 592 TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER PRO SEQRES 20 A 592 LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN LEU SEQRES 21 A 592 PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SER SEQRES 22 A 592 ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU ILE SEQRES 23 A 592 VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS LEU SEQRES 24 A 592 GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL ARG SEQRES 25 A 592 PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN ALA SEQRES 26 A 592 LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO ASN SEQRES 27 A 592 LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG LYS SEQRES 28 A 592 ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP LEU SEQRES 29 A 592 ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG VAL SEQRES 30 A 592 LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU ALA SEQRES 31 A 592 PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA MET SEQRES 32 A 592 ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO ASN SEQRES 33 A 592 MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE VAL SEQRES 34 A 592 TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU ASN SEQRES 35 A 592 ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG TYR SEQRES 36 A 592 PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU ASN SEQRES 37 A 592 ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR THR SEQRES 38 A 592 LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SER SEQRES 39 A 592 ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET ALA SEQRES 40 A 592 MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE ILE SEQRES 41 A 592 LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS GLU SEQRES 42 A 592 GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS ASP SEQRES 43 A 592 GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU ARG SEQRES 44 A 592 LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA VAL SEQRES 45 A 592 THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR GLY SEQRES 46 A 592 SER THR TRP TYR ASP ALA LYS SEQRES 1 B 12 DG DC DG DA DT DC DA DC DG DT DA C SEQRES 1 C 16 DG DA DC DG DT DA DC DG DT DG DA DT DC SEQRES 2 C 16 DG DC DA HET CTP A 901 41 HET SO4 A 902 5 HET SO4 A 903 5 HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 4 CTP C9 H16 N3 O14 P3 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *857(H2 O) HELIX 1 1 THR A 308 ALA A 313 5 6 HELIX 2 2 ARG A 347 LEU A 352 1 6 HELIX 3 3 ASP A 354 ASP A 363 1 10 HELIX 4 4 ASP A 372 LYS A 383 1 12 HELIX 5 5 LEU A 394 ASP A 402 1 9 HELIX 6 6 PRO A 403 GLY A 406 5 4 HELIX 7 7 ASP A 409 MET A 416 1 8 HELIX 8 8 PRO A 424 GLY A 430 1 7 HELIX 9 9 LYS A 431 ARG A 435 5 5 HELIX 10 10 ASP A 439 ASN A 468 1 30 HELIX 11 11 GLN A 470 LEU A 477 1 8 HELIX 12 12 LEU A 477 GLY A 492 1 16 HELIX 13 13 ASP A 496 GLY A 523 1 28 HELIX 14 14 SER A 530 GLU A 540 1 11 HELIX 15 15 SER A 557 ALA A 565 1 9 HELIX 16 16 PRO A 566 HIS A 568 5 3 HELIX 17 17 GLU A 569 ILE A 588 1 20 HELIX 18 18 ILE A 588 VAL A 595 1 8 HELIX 19 19 LEU A 630 LYS A 635 1 6 HELIX 20 20 ILE A 636 GLN A 638 5 3 HELIX 21 21 GLN A 656 GLU A 667 1 12 HELIX 22 22 ASP A 668 ARG A 677 1 10 HELIX 23 23 ASP A 680 GLN A 691 1 12 HELIX 24 24 SER A 693 VAL A 697 5 5 HELIX 25 25 THR A 698 GLY A 715 1 18 HELIX 26 26 SER A 717 ASN A 726 1 10 HELIX 27 27 SER A 728 PHE A 743 1 16 HELIX 28 28 PHE A 743 GLY A 761 1 19 HELIX 29 29 PRO A 774 SER A 778 5 5 HELIX 30 30 ASN A 780 GLU A 818 1 39 HELIX 31 31 GLU A 840 GLN A 854 1 15 SHEET 1 A 6 THR A 302 LEU A 303 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 O PHE A 345 N THR A 302 SHEET 3 A 6 GLY A 334 ASN A 339 -1 N VAL A 337 O PHE A 344 SHEET 4 A 6 LYS A 315 GLU A 321 -1 N ALA A 317 O VAL A 338 SHEET 5 A 6 LYS A 367 MET A 370 1 O SER A 369 N LEU A 318 SHEET 6 A 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 B 3 LYS A 601 VAL A 602 0 SHEET 2 B 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 B 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 C 2 ILE A 605 ASN A 607 0 SHEET 2 C 2 SER A 617 THR A 619 -1 O THR A 619 N ILE A 605 SHEET 1 D 4 HIS A 823 GLN A 827 0 SHEET 2 D 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 D 4 TRP A 647 TYR A 654 -1 N PHE A 650 O LEU A 834 SHEET 4 D 4 VAL A 864 GLY A 869 -1 O HIS A 867 N ALA A 651 SHEET 1 E 2 TYR A 762 THR A 764 0 SHEET 2 E 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 CISPEP 1 GLU A 620 PRO A 621 0 2.78 SITE 1 AC1 10 GLU A 469 GLN A 470 ASP A 471 ARG A 472 SITE 2 AC1 10 LEU A 473 LEU A 767 HIS A 768 HOH A1168 SITE 3 AC1 10 HOH A1280 HOH A1443 SITE 1 AC2 3 ARG A 702 LYS A 706 HOH A1764 SITE 1 AC3 7 MET A 299 ALA A 300 ARG A 343 ARG A 677 SITE 2 AC3 7 HOH A1320 HOH A1515 HOH A1750 CRYST1 88.410 93.410 105.760 90.00 90.00 90.00 P 21 21 21 4 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 0.011311 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009455 0.00000 MASTER 527 0 3 31 17 0 6 6 0 0 0 49 END