HEADER TRANSFERASE 01-AUG-17 5OMV TITLE TERNARY COMPLEX OF 9N DNA POLYMERASE IN THE REPLICATIVE STATE WITH TWO TITLE 2 METAL IONS IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA TEMPLATE; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA PRIMER; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS SP. 9ON-7; SOURCE 3 ORGANISM_TAXID: 103799; SOURCE 4 GENE: POL, POLA; 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 TERNARY COMPLEX, DNA POLYMERASE, TRIPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,A.MARX,K.DIEDERICHS REVDAT 3 17-JAN-24 5OMV 1 LINK REVDAT 2 12-SEP-18 5OMV 1 REMARK REVDAT 1 20-DEC-17 5OMV 0 JRNL AUTH H.M.KROPP,K.BETZ,J.WIRTH,K.DIEDERICHS,A.MARX JRNL TITL CRYSTAL STRUCTURES OF TERNARY COMPLEXES OF ARCHAEAL B-FAMILY JRNL TITL 2 DNA POLYMERASES. JRNL REF PLOS ONE V. 12 88005 2017 JRNL REFN ESSN 1932-6203 JRNL PMID 29211756 JRNL DOI 10.1371/JOURNAL.PONE.0188005 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC0_2787: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 130623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 6604 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 47.4953 - 6.2188 1.00 4145 218 0.1349 0.1765 REMARK 3 2 6.2188 - 4.9377 1.00 4140 211 0.1365 0.2075 REMARK 3 3 4.9377 - 4.3140 1.00 4106 225 0.1138 0.1435 REMARK 3 4 4.3140 - 3.9198 1.00 4128 229 0.1242 0.1377 REMARK 3 5 3.9198 - 3.6390 1.00 4127 224 0.1534 0.2137 REMARK 3 6 3.6390 - 3.4245 1.00 4151 244 0.1698 0.2192 REMARK 3 7 3.4245 - 3.2530 1.00 4154 203 0.1688 0.1876 REMARK 3 8 3.2530 - 3.1114 1.00 4152 225 0.1785 0.2522 REMARK 3 9 3.1114 - 2.9917 1.00 4117 208 0.1989 0.2473 REMARK 3 10 2.9917 - 2.8885 1.00 4093 240 0.1942 0.2680 REMARK 3 11 2.8885 - 2.7982 1.00 4200 214 0.2192 0.2967 REMARK 3 12 2.7982 - 2.7182 1.00 4107 254 0.2192 0.2712 REMARK 3 13 2.7182 - 2.6466 1.00 4084 244 0.2278 0.2515 REMARK 3 14 2.6466 - 2.5821 1.00 4140 231 0.2281 0.3096 REMARK 3 15 2.5821 - 2.5234 1.00 4082 254 0.2311 0.3044 REMARK 3 16 2.5234 - 2.4697 1.00 4171 206 0.2456 0.3045 REMARK 3 17 2.4697 - 2.4203 1.00 4127 223 0.2617 0.3184 REMARK 3 18 2.4203 - 2.3746 1.00 4112 196 0.2707 0.3038 REMARK 3 19 2.3746 - 2.3322 1.00 4189 201 0.2860 0.3020 REMARK 3 20 2.3322 - 2.2927 0.99 4126 221 0.3001 0.3499 REMARK 3 21 2.2927 - 2.2557 0.99 4123 226 0.3176 0.3642 REMARK 3 22 2.2557 - 2.2210 0.99 4136 227 0.3268 0.3241 REMARK 3 23 2.2210 - 2.1883 1.00 4136 188 0.3343 0.4073 REMARK 3 24 2.1883 - 2.1575 1.00 4144 210 0.3497 0.3870 REMARK 3 25 2.1575 - 2.1283 1.00 4170 199 0.3691 0.4080 REMARK 3 26 2.1283 - 2.1007 1.00 4149 208 0.3716 0.3760 REMARK 3 27 2.1007 - 2.0744 1.00 4117 189 0.3869 0.4181 REMARK 3 28 2.0744 - 2.0494 1.00 4211 215 0.4114 0.4113 REMARK 3 29 2.0494 - 2.0256 1.00 4069 233 0.4316 0.4269 REMARK 3 30 2.0256 - 2.0028 0.99 4113 238 0.4529 0.4945 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.830 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 : 0.008 7033 REMARK 3 ANGLE : 0.924 9602 REMARK 3 CHIRALITY : 0.053 1025 REMARK 3 PLANARITY : 0.005 1146 REMARK 3 DIHEDRAL : 13.433 4162 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 1 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 109.8299 96.9093 3.4624 REMARK 3 T TENSOR REMARK 3 T11: 0.2734 T22: 0.3834 REMARK 3 T33: 0.3359 T12: 0.0355 REMARK 3 T13: 0.0364 T23: 0.0581 REMARK 3 L TENSOR REMARK 3 L11: 1.4945 L22: 1.4585 REMARK 3 L33: 1.7854 L12: 0.8134 REMARK 3 L13: 0.8959 L23: 0.6498 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: 0.0700 S13: -0.1314 REMARK 3 S21: -0.0215 S22: 0.0169 S23: -0.2829 REMARK 3 S31: 0.1040 S32: 0.2189 S33: -0.0186 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): 109.7231 108.2311 17.5322 REMARK 3 T TENSOR REMARK 3 T11: 0.3745 T22: 0.4876 REMARK 3 T33: 0.3986 T12: 0.0057 REMARK 3 T13: -0.0794 T23: 0.0673 REMARK 3 L TENSOR REMARK 3 L11: 2.7505 L22: 2.0466 REMARK 3 L33: 1.1108 L12: 1.4585 REMARK 3 L13: 0.0924 L23: 0.3147 REMARK 3 S TENSOR REMARK 3 S11: -0.0075 S12: -0.2308 S13: 0.3366 REMARK 3 S21: 0.0674 S22: -0.1327 S23: 0.0115 REMARK 3 S31: -0.2055 S32: 0.1299 S33: 0.1439 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 364 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.8219 94.4660 23.9556 REMARK 3 T TENSOR REMARK 3 T11: 0.3780 T22: 0.3474 REMARK 3 T33: 0.3460 T12: -0.0567 REMARK 3 T13: 0.0012 T23: 0.0737 REMARK 3 L TENSOR REMARK 3 L11: 1.3253 L22: 0.6743 REMARK 3 L33: 2.8903 L12: -0.1897 REMARK 3 L13: -0.7870 L23: 0.4212 REMARK 3 S TENSOR REMARK 3 S11: -0.1076 S12: -0.0294 S13: -0.2052 REMARK 3 S21: 0.1287 S22: -0.0322 S23: 0.0522 REMARK 3 S31: 0.2803 S32: -0.1819 S33: 0.1507 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 589 THROUGH 758 ) REMARK 3 ORIGIN FOR THE GROUP (A): 87.4639 126.9784 29.4918 REMARK 3 T TENSOR REMARK 3 T11: 0.3188 T22: 0.4088 REMARK 3 T33: 0.4541 T12: 0.0087 REMARK 3 T13: -0.0472 T23: -0.0683 REMARK 3 L TENSOR REMARK 3 L11: 2.8164 L22: 2.9036 REMARK 3 L33: 3.8168 L12: 0.3670 REMARK 3 L13: -0.0524 L23: -0.8431 REMARK 3 S TENSOR REMARK 3 S11: -0.0272 S12: -0.2863 S13: 0.4157 REMARK 3 S21: 0.1890 S22: 0.0890 S23: -0.3344 REMARK 3 S31: -0.4445 S32: 0.2259 S33: -0.0640 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 2 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.7406 118.3922 14.7602 REMARK 3 T TENSOR REMARK 3 T11: 0.3864 T22: 0.4355 REMARK 3 T33: 0.4077 T12: 0.0042 REMARK 3 T13: 0.0254 T23: 0.0736 REMARK 3 L TENSOR REMARK 3 L11: 0.4991 L22: 2.4995 REMARK 3 L33: 1.6936 L12: -0.3514 REMARK 3 L13: 0.8167 L23: -1.2431 REMARK 3 S TENSOR REMARK 3 S11: 0.0706 S12: 0.1835 S13: 0.1249 REMARK 3 S21: -0.1727 S22: -0.0728 S23: -0.3896 REMARK 3 S31: -0.2358 S32: -0.1962 S33: -0.1221 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.4113 121.0118 17.0810 REMARK 3 T TENSOR REMARK 3 T11: 0.4510 T22: 0.4651 REMARK 3 T33: 0.3742 T12: 0.0179 REMARK 3 T13: -0.0369 T23: 0.0298 REMARK 3 L TENSOR REMARK 3 L11: 2.0449 L22: 3.0083 REMARK 3 L33: 1.6208 L12: -2.4524 REMARK 3 L13: 0.6619 L23: -1.2148 REMARK 3 S TENSOR REMARK 3 S11: 0.1372 S12: 0.3764 S13: 0.0802 REMARK 3 S21: -0.1300 S22: -0.2161 S23: 0.0809 REMARK 3 S31: -0.2970 S32: -0.0232 S33: 0.0927 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 5OMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999973488495 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 130652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.482 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4K8X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5, REMARK 280 6% ISOPROPANOL, 36% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.0K 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 33.34400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.36750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.48200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.36750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.34400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.48200 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 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: 7120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 LYS A 759 REMARK 465 THR A 760 REMARK 465 LYS A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 GLY A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 VAL A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 LYS A 774 REMARK 465 LYS A 775 REMARK 465 DA T 1 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 DC P 12 O3' 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 NH1 ARG A 713 OD2 ASP A 728 2.01 REMARK 500 OE2 GLU A 354 OH TYR A 496 2.18 REMARK 500 O VAL A 698 O HOH A 901 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 DC T 3 O3' DC T 3 C3' -0.059 REMARK 500 DC P 9 O3' DC P 9 C3' -0.043 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 DC P 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 67 137.23 -170.57 REMARK 500 PHE A 214 -69.24 -125.99 REMARK 500 SER A 407 59.81 37.49 REMARK 500 GLU A 436 -54.20 75.78 REMARK 500 TRP A 504 44.42 -89.60 REMARK 500 CYS A 506 92.97 -164.72 REMARK 500 THR A 541 -60.92 64.37 REMARK 500 LYS A 592 -7.09 74.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE A 804 REMARK 610 PGE A 805 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 MN A 801 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD1 REMARK 620 2 PHE A 405 O 82.8 REMARK 620 3 ASP A 542 OD2 91.2 85.2 REMARK 620 4 DTP A 806 O3G 88.2 87.5 172.7 REMARK 620 5 DTP A 806 O2B 170.5 89.1 93.0 86.5 REMARK 620 6 DTP A 806 O2A 96.5 177.5 97.2 90.1 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD2 REMARK 620 2 ASP A 542 OD1 107.9 REMARK 620 3 DTP A 806 O2A 96.5 77.8 REMARK 620 4 HOH A1001 O 101.2 101.9 161.4 REMARK 620 5 HOH A1031 O 85.5 151.2 75.3 100.2 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 MN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTP A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG T 101 DBREF 5OMV A 1 775 UNP Q56366 DPOL_THES9 1 775 DBREF 5OMV T 1 16 PDB 5OMV 5OMV 1 16 DBREF 5OMV P 1 10 PDB 5OMV 5OMV 1 10 SEQADV 5OMV ALA A 141 UNP Q56366 ASP 141 ENGINEERED MUTATION SEQADV 5OMV ALA A 143 UNP Q56366 GLU 143 ENGINEERED MUTATION SEQRES 1 A 775 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASN GLY LYS SEQRES 2 A 775 PRO VAL ILE ARG VAL PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 775 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 775 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU ASP VAL LYS SEQRES 5 A 775 LYS VAL THR ALA LYS ARG HIS GLY THR VAL VAL LYS VAL SEQRES 6 A 775 LYS ARG ALA GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 775 PRO ILE GLU VAL TRP LYS LEU TYR PHE ASN HIS PRO GLN SEQRES 8 A 775 ASP VAL PRO ALA ILE ARG ASP ARG ILE ARG ALA HIS PRO SEQRES 9 A 775 ALA VAL VAL ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 775 LYS ARG TYR LEU ILE ASP LYS GLY LEU ILE PRO MET GLU SEQRES 11 A 775 GLY ASP GLU GLU LEU THR MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 775 THR LEU TYR HIS GLU GLY GLU GLU PHE GLY THR GLY PRO SEQRES 13 A 775 ILE LEU MET ILE SER TYR ALA ASP GLY SER GLU ALA ARG SEQRES 14 A 775 VAL ILE THR TRP LYS LYS ILE ASP LEU PRO TYR VAL ASP SEQRES 15 A 775 VAL VAL SER THR GLU LYS GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 775 ARG VAL VAL ARG GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 775 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 775 ARG CYS GLU GLU LEU GLY ILE LYS PHE THR LEU GLY ARG SEQRES 19 A 775 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 775 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 775 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 775 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY LYS PRO SEQRES 23 A 775 LYS GLU LYS VAL TYR ALA GLU GLU ILE ALA GLN ALA TRP SEQRES 24 A 775 GLU SER GLY GLU GLY LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 775 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY ARG GLU SEQRES 26 A 775 PHE PHE PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 775 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 775 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR LYS ARG SEQRES 29 A 775 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU ARG GLU LEU SEQRES 30 A 775 ALA ARG ARG ARG GLY GLY TYR ALA GLY GLY TYR VAL LYS SEQRES 31 A 775 GLU PRO GLU ARG GLY LEU TRP ASP ASN ILE VAL TYR LEU SEQRES 32 A 775 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 775 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 775 GLU TYR ASP VAL ALA PRO GLU VAL GLY HIS LYS PHE CYS SEQRES 35 A 775 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 775 LEU LEU GLU GLU ARG GLN LYS ILE LYS ARG LYS MET LYS SEQRES 37 A 775 ALA THR VAL ASP PRO LEU GLU LYS LYS LEU LEU ASP TYR SEQRES 38 A 775 ARG GLN ARG ALA ILE LYS ILE LEU ALA ASN SER PHE TYR SEQRES 39 A 775 GLY TYR TYR GLY TYR ALA LYS ALA ARG TRP TYR CYS LYS SEQRES 40 A 775 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 775 ILE GLU MET VAL ILE ARG GLU LEU GLU GLU LYS PHE GLY SEQRES 42 A 775 PHE LYS VAL LEU TYR ALA ASP THR ASP GLY LEU HIS ALA SEQRES 43 A 775 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 775 ALA LYS GLU PHE LEU LYS TYR ILE ASN PRO LYS LEU PRO SEQRES 45 A 775 GLY LEU LEU GLU LEU GLU TYR GLU GLY PHE TYR VAL ARG SEQRES 46 A 775 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 775 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 775 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 775 ARG VAL LEU GLU ALA ILE LEU LYS HIS GLY ASP VAL GLU SEQRES 50 A 775 GLU ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 775 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 775 GLU GLN ILE THR ARG ASP LEU ARG ASP TYR LYS ALA THR SEQRES 53 A 775 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 775 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 775 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 775 PRO ALA ASP GLU PHE ASP PRO THR LYS HIS ARG TYR ASP SEQRES 57 A 775 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 775 GLU ARG ILE LEU LYS ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 775 LEU ARG TYR GLN LYS THR LYS GLN VAL GLY LEU GLY ALA SEQRES 60 A 775 TRP LEU LYS VAL LYS GLY LYS LYS SEQRES 1 T 16 DA DA DC DT DG DT DG DG DC DC DG DT DG SEQRES 2 T 16 DG DT DC SEQRES 1 P 12 DG DA DC DC DA DC DG DG DC DC DA DC HET MN A 801 1 HET GOL A 802 6 HET MG A 803 1 HET PGE A 804 7 HET PGE A 805 7 HET DTP A 806 42 HET MG T 101 1 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MN MN 2+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 MG 2(MG 2+) FORMUL 7 PGE 2(C6 H14 O4) FORMUL 9 DTP C10 H16 N5 O12 P3 FORMUL 11 HOH *179(H2 O) HELIX 1 AA1 ASP A 44 SER A 46 5 3 HELIX 2 AA2 ALA A 47 LYS A 52 1 6 HELIX 3 AA3 GLN A 91 HIS A 103 1 13 HELIX 4 AA4 PRO A 115 LYS A 124 1 10 HELIX 5 AA5 THR A 186 ASP A 202 1 17 HELIX 6 AA6 PHE A 214 GLY A 227 1 14 HELIX 7 AA7 LEU A 260 ILE A 268 1 9 HELIX 8 AA8 THR A 274 GLY A 284 1 11 HELIX 9 AA9 TYR A 291 GLY A 302 1 12 HELIX 10 AB1 GLY A 304 GLY A 338 1 35 HELIX 11 AB2 SER A 340 SER A 345 1 6 HELIX 12 AB3 SER A 348 ASN A 365 1 18 HELIX 13 AB4 ASP A 373 ARG A 380 1 8 HELIX 14 AB5 SER A 407 ASN A 417 1 11 HELIX 15 AB6 GLY A 447 THR A 470 1 24 HELIX 16 AB7 ASP A 472 GLY A 498 1 27 HELIX 17 AB8 CYS A 506 PHE A 532 1 27 HELIX 18 AB9 ASP A 552 ASN A 568 1 17 HELIX 19 AC1 PRO A 569 LEU A 571 5 3 HELIX 20 AC2 LEU A 608 ARG A 612 5 5 HELIX 21 AC3 SER A 616 GLY A 634 1 19 HELIX 22 AC4 ASP A 635 LYS A 652 1 18 HELIX 23 AC5 PRO A 656 VAL A 661 5 6 HELIX 24 AC6 ASP A 669 TYR A 673 5 5 HELIX 25 AC7 GLY A 677 ARG A 689 1 13 HELIX 26 AC8 ARG A 709 ASP A 712 5 4 HELIX 27 AC9 ASP A 718 PHE A 720 5 3 HELIX 28 AD1 ASP A 728 ASN A 735 1 8 HELIX 29 AD2 GLN A 736 LYS A 746 1 11 HELIX 30 AD3 ALA A 747 GLY A 749 5 3 HELIX 31 AD4 ARG A 751 LEU A 755 5 5 SHEET 1 AA1 3 ILE A 2 GLU A 10 0 SHEET 2 AA1 3 LYS A 13 GLU A 22 -1 O VAL A 15 N ILE A 8 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O GLU A 29 N VAL A 18 SHEET 1 AA2 4 ARG A 67 PHE A 75 0 SHEET 2 AA2 4 ARG A 78 TYR A 86 -1 O LYS A 84 N GLU A 69 SHEET 3 AA2 4 TYR A 37 LEU A 42 -1 N PHE A 38 O LEU A 85 SHEET 4 AA2 4 VAL A 106 TYR A 110 -1 O ASP A 108 N LEU A 41 SHEET 1 AA3 2 THR A 55 ARG A 58 0 SHEET 2 AA3 2 THR A 61 LYS A 64 -1 O VAL A 63 N ALA A 56 SHEET 1 AA4 6 VAL A 181 VAL A 183 0 SHEET 2 AA4 6 ALA A 168 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ALA A 163 -1 N ILE A 160 O ILE A 171 SHEET 4 AA4 6 MET A 137 THR A 144 -1 N ALA A 143 O LEU A 158 SHEET 5 AA4 6 VAL A 205 THR A 208 1 O ILE A 207 N LEU A 138 SHEET 6 AA4 6 ILE A 256 ASP A 259 1 O PHE A 258 N LEU A 206 SHEET 1 AA5 2 LYS A 240 MET A 244 0 SHEET 2 AA5 2 ARG A 247 GLU A 251 -1 O GLU A 251 N LYS A 240 SHEET 1 AA6 7 VAL A 389 LYS A 390 0 SHEET 2 AA6 7 LYS A 535 ASP A 540 -1 O ALA A 539 N LYS A 390 SHEET 3 AA6 7 GLY A 543 THR A 547 -1 O THR A 547 N LYS A 535 SHEET 4 AA6 7 LEU A 396 PHE A 405 -1 N VAL A 401 O ALA A 546 SHEET 5 AA6 7 LEU A 577 THR A 590 -1 O GLY A 586 N TRP A 397 SHEET 6 AA6 7 LYS A 593 ASP A 598 -1 O ALA A 595 N PHE A 587 SHEET 7 AA6 7 ILE A 603 ARG A 606 -1 O THR A 604 N VAL A 596 SHEET 1 AA7 2 TYR A 431 VAL A 433 0 SHEET 2 AA7 2 LYS A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 AA8 3 ILE A 662 GLN A 665 0 SHEET 2 AA8 3 VAL A 698 VAL A 703 -1 O ILE A 699 N GLU A 664 SHEET 3 AA8 3 ALA A 714 PRO A 716 -1 O ILE A 715 N ILE A 702 LINK OD1 ASP A 404 MN MN A 801 1555 1555 2.13 LINK OD2 ASP A 404 MG MG A 803 1555 1555 2.20 LINK O PHE A 405 MN MN A 801 1555 1555 2.21 LINK OD2 ASP A 542 MN MN A 801 1555 1555 2.14 LINK OD1 ASP A 542 MG MG A 803 1555 1555 2.25 LINK MN MN A 801 O3G DTP A 806 1555 1555 2.19 LINK MN MN A 801 O2B DTP A 806 1555 1555 2.20 LINK MN MN A 801 O2A DTP A 806 1555 1555 2.28 LINK MG MG A 803 O2A DTP A 806 1555 1555 2.59 LINK MG MG A 803 O HOH A1001 1555 1555 2.36 LINK MG MG A 803 O HOH A1031 1555 1555 2.72 LINK O3' DC T 16 MG MG T 101 1555 1555 2.01 SITE 1 AC1 4 ASP A 404 PHE A 405 ASP A 542 DTP A 806 SITE 1 AC2 6 TYR A 402 HIS A 545 TYR A 583 TYR A 594 SITE 2 AC2 6 ARG A 606 DC P 12 SITE 1 AC3 7 TYR A 402 ASP A 404 ASP A 542 DTP A 806 SITE 2 AC3 7 HOH A1001 HOH A1031 DC P 12 SITE 1 AC4 2 TYR A 273 HOH A1038 SITE 1 AC5 1 TYR A 110 SITE 1 AC6 19 ASP A 404 PHE A 405 SER A 407 LEU A 408 SITE 2 AC6 19 TYR A 409 ARG A 460 LYS A 487 ASN A 491 SITE 3 AC6 19 ASP A 542 MN A 801 MG A 803 HOH A 922 SITE 4 AC6 19 HOH A 935 HOH A 947 HOH A 975 HOH A 986 SITE 5 AC6 19 DC P 12 DT T 4 DG T 5 SITE 1 AC7 2 ARG A 97 DC T 16 CRYST1 66.688 94.964 158.735 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 0.014995 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006300 0.00000