10 20 30 40 50 60 70 80 4DQS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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