HEADER REPLICATION 21-MAY-21 7OM3 TITLE CRYSTAL STRUCTURE OF KOD DNA POLYMERASE IN A BINARY COMPLEX WITH TITLE 2 HYPOXANTHINE CONTAINING TEMPLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE,DNA POLYMERASE,DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,2.7.7.7,2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 21NT TEMPLATE; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PRIMER; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS KOD1; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 GENE: POL, TK0001; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET24A; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS HYPOXANTHINE, BINARY COMPLEX, DNA POLYMERASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,H.M.KROPP,K.DIEDERICHS,A.MARX REVDAT 3 31-JAN-24 7OM3 1 REMARK REVDAT 2 17-NOV-21 7OM3 1 JRNL REVDAT 1 13-OCT-21 7OM3 0 JRNL AUTH H.M.KROPP,S.LUDMANN,K.DIEDERICHS,K.BETZ,A.MARX JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF DEAMINATED JRNL TITL 2 NUCLEOBASES BY AN ARCHAEAL DNA POLYMERASE. JRNL REF CHEMBIOCHEM V. 22 3060 2021 JRNL REFN ESSN 1439-7633 JRNL PMID 34486208 JRNL DOI 10.1002/CBIC.202100306 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4085 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 144954 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) : 0.183 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.550 REMARK 3 FREE R VALUE TEST SET COUNT : 3691 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 44.4500 - 5.6900 1.00 5847 159 0.1598 0.2513 REMARK 3 2 5.6900 - 4.5200 1.00 5900 155 0.1253 0.1395 REMARK 3 3 4.5200 - 3.9500 1.00 5861 150 0.1224 0.1699 REMARK 3 4 3.9500 - 3.5800 1.00 5909 158 0.1435 0.2076 REMARK 3 5 3.5800 - 3.3300 1.00 5866 154 0.1532 0.2063 REMARK 3 6 3.3300 - 3.1300 1.00 5869 150 0.1780 0.2062 REMARK 3 7 3.1300 - 2.9700 1.00 5843 153 0.1862 0.2626 REMARK 3 8 2.9700 - 2.8500 1.00 5878 153 0.1811 0.2272 REMARK 3 9 2.8500 - 2.7400 1.00 5868 154 0.1870 0.2496 REMARK 3 10 2.7400 - 2.6400 1.00 5897 156 0.1965 0.2692 REMARK 3 11 2.6400 - 2.5600 1.00 5923 153 0.2081 0.2682 REMARK 3 12 2.5600 - 2.4900 1.00 5864 154 0.2110 0.2738 REMARK 3 13 2.4900 - 2.4200 1.00 5798 151 0.2141 0.2689 REMARK 3 14 2.4200 - 2.3600 1.00 5940 160 0.2198 0.2661 REMARK 3 15 2.3600 - 2.3100 1.00 5879 153 0.2326 0.2732 REMARK 3 16 2.3100 - 2.2600 1.00 5867 158 0.2356 0.2629 REMARK 3 17 2.2600 - 2.2100 1.00 5895 152 0.2578 0.3302 REMARK 3 18 2.2100 - 2.1700 0.99 5864 155 0.2741 0.3447 REMARK 3 19 2.1700 - 2.1300 0.99 5804 150 0.2899 0.3358 REMARK 3 20 2.1300 - 2.1000 0.96 5663 146 0.3123 0.3876 REMARK 3 21 2.1000 - 2.0600 0.93 5424 141 0.3281 0.3615 REMARK 3 22 2.0600 - 2.0300 0.86 5102 130 0.3494 0.3389 REMARK 3 23 2.0300 - 2.0000 0.80 4669 121 0.3501 0.3595 REMARK 3 24 2.0000 - 1.9700 0.73 4283 112 0.3547 0.3973 REMARK 3 25 1.9700 - 1.9500 0.57 3357 88 0.3723 0.4200 REMARK 3 26 1.9500 - 1.9200 0.20 1193 25 0.3582 0.3812 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) : 0.308 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.00 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 : 0.012 7155 REMARK 3 ANGLE : 1.214 9780 REMARK 3 CHIRALITY : 0.061 1047 REMARK 3 PLANARITY : 0.012 1139 REMARK 3 DIHEDRAL : 18.224 2788 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4067 35.1920 5.9875 REMARK 3 T TENSOR REMARK 3 T11: 0.2020 T22: 0.1941 REMARK 3 T33: 0.2313 T12: 0.0138 REMARK 3 T13: -0.0450 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.4795 L22: 0.6547 REMARK 3 L33: 2.3803 L12: 0.3560 REMARK 3 L13: -1.4285 L23: -0.6253 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: 0.2301 S13: 0.1336 REMARK 3 S21: -0.0755 S22: 0.0193 S23: 0.0018 REMARK 3 S31: -0.0326 S32: -0.1063 S33: -0.0258 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 304 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0700 22.9887 21.6395 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.2550 REMARK 3 T33: 0.2186 T12: -0.0027 REMARK 3 T13: 0.0291 T23: -0.0674 REMARK 3 L TENSOR REMARK 3 L11: 3.7549 L22: 2.7601 REMARK 3 L33: 1.6674 L12: 0.3013 REMARK 3 L13: -0.2463 L23: -1.1785 REMARK 3 S TENSOR REMARK 3 S11: -0.0758 S12: 0.0737 S13: -0.3105 REMARK 3 S21: -0.2038 S22: 0.0256 S23: -0.0657 REMARK 3 S31: 0.2558 S32: -0.1259 S33: 0.0611 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 305 THROUGH 552 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9045 24.8370 16.2507 REMARK 3 T TENSOR REMARK 3 T11: 0.2597 T22: 0.3139 REMARK 3 T33: 0.3134 T12: -0.0119 REMARK 3 T13: 0.0013 T23: 0.0373 REMARK 3 L TENSOR REMARK 3 L11: 0.7511 L22: 0.5076 REMARK 3 L33: 0.3670 L12: -0.0989 REMARK 3 L13: 0.1027 L23: -0.1383 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: -0.1015 S13: -0.0475 REMARK 3 S21: 0.0177 S22: -0.0374 S23: -0.1511 REMARK 3 S31: 0.0482 S32: 0.0893 S33: 0.0330 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 553 THROUGH 759 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4305 2.9463 31.9155 REMARK 3 T TENSOR REMARK 3 T11: 0.3137 T22: 0.3270 REMARK 3 T33: 0.4053 T12: 0.0198 REMARK 3 T13: 0.0407 T23: 0.0482 REMARK 3 L TENSOR REMARK 3 L11: 3.7889 L22: 1.7251 REMARK 3 L33: 0.9224 L12: 1.6120 REMARK 3 L13: -0.0749 L23: -0.0232 REMARK 3 S TENSOR REMARK 3 S11: 0.1600 S12: -0.4840 S13: -0.3875 REMARK 3 S21: 0.2526 S22: -0.1939 S23: -0.0138 REMARK 3 S31: 0.1042 S32: -0.0436 S33: 0.0419 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7740 29.9814 -2.0137 REMARK 3 T TENSOR REMARK 3 T11: 0.4715 T22: 0.5027 REMARK 3 T33: 0.5231 T12: -0.0701 REMARK 3 T13: -0.0234 T23: 0.0672 REMARK 3 L TENSOR REMARK 3 L11: 5.2673 L22: 2.8134 REMARK 3 L33: 3.6249 L12: -3.4276 REMARK 3 L13: 3.9459 L23: -1.9497 REMARK 3 S TENSOR REMARK 3 S11: 0.0859 S12: -0.2858 S13: -2.0029 REMARK 3 S21: 0.0460 S22: 0.4736 S23: 0.6155 REMARK 3 S31: 1.3169 S32: -0.7014 S33: -0.6959 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 7 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.1686 1.6841 14.3192 REMARK 3 T TENSOR REMARK 3 T11: 0.2577 T22: 0.3388 REMARK 3 T33: 0.5496 T12: 0.0335 REMARK 3 T13: 0.0156 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.2272 L22: 3.7232 REMARK 3 L33: 3.5761 L12: 1.8904 REMARK 3 L13: -1.1449 L23: 1.2308 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: 0.3719 S13: -0.1266 REMARK 3 S21: -0.0398 S22: -0.0692 S23: 0.5280 REMARK 3 S31: 0.2598 S32: -0.2457 S33: 0.0661 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.7798 -3.9092 16.5505 REMARK 3 T TENSOR REMARK 3 T11: 0.3400 T22: 0.4215 REMARK 3 T33: 0.7444 T12: -0.0175 REMARK 3 T13: 0.1403 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.5347 L22: 8.6096 REMARK 3 L33: 3.3068 L12: 0.7654 REMARK 3 L13: 1.0477 L23: 1.7858 REMARK 3 S TENSOR REMARK 3 S11: 0.1193 S12: 0.1699 S13: -0.8833 REMARK 3 S21: -0.7954 S22: -0.1007 S23: -1.0896 REMARK 3 S31: 0.2102 S32: -0.0118 S33: -0.0362 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 7OM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.0000089622351307 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 147921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 48.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4K8Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS E7: 0.12 M ETHYLENE GLYCOLS REMARK 280 (0.3 M DIETHYLENE GLYCOL, 0.3 M TRIETHYLENE GLYCOL, 0.3 M REMARK 280 TETRAETHYLENE GLYCOL, 0.3 M PENTAETHYLENE GLYCOL), 0.1 M SODIUM REMARK 280 HEPES/MOPS PH 7.5, 50 % (V/V) OF A MIXTURE OF GLYCEROL (40 % V/V) REMARK 280 AND PEG 4000 (20 % W/V)., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 56.67800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 71.46800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 56.67800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 71.46800 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: 8450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 A1335 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 760 REMARK 465 ARG A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 PRO A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 THR A 774 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 SER A 312 O HOH A 1012 1.52 REMARK 500 HH TYR A 579 O HOH A 1007 1.52 REMARK 500 HH TYR A 30 O HOH A 1019 1.57 REMARK 500 HZ3 LYS A 20 OE1 GLU A 29 1.60 REMARK 500 OP2 DC T 21 O HOH T 101 1.91 REMARK 500 O HOH A 1286 O HOH A 1336 2.04 REMARK 500 O HOH A 1182 O HOH A 1299 2.09 REMARK 500 O HOH A 1004 O HOH A 1319 2.12 REMARK 500 O HOH A 1255 O HOH A 1287 2.12 REMARK 500 OD2 ASP A 721 O HOH A 1001 2.14 REMARK 500 O HOH A 1232 O HOH A 1314 2.14 REMARK 500 NH2 ARG A 266 OE1 GLU A 330 2.16 REMARK 500 O VAL A 106 O HOH A 1002 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 DI T 4 O3' DI T 4 C3' -0.207 REMARK 500 DI T 4 C6 DI T 4 O6 0.137 REMARK 500 DT T 9 O3' DT T 9 C3' -0.043 REMARK 500 DC P 4 O3' DC P 4 C3' -0.048 REMARK 500 DC P 9 O3' DC P 9 C3' -0.058 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 DT T 3 O3' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DI T 4 O5' - P - OP1 ANGL. DEV. = 11.3 DEGREES REMARK 500 DI T 4 O5' - P - OP2 ANGL. DEV. = 9.8 DEGREES REMARK 500 DC T 5 O5' - P - OP1 ANGL. DEV. = -9.4 DEGREES REMARK 500 DA T 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT T 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC T 15 O3' - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 DC T 15 O5' - P - OP2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG T 19 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC P 9 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DOC P 12 O3' - P - OP2 ANGL. DEV. = 11.4 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 HIS A 59 57.21 33.96 REMARK 500 PHE A 214 -64.49 -127.21 REMARK 500 ARG A 380 2.70 -69.45 REMARK 500 ASN A 399 67.34 62.51 REMARK 500 SER A 407 66.73 34.54 REMARK 500 GLN A 436 -55.25 62.03 REMARK 500 THR A 541 -67.41 73.84 REMARK 500 ARG A 689 -158.62 -83.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 7OM3 A 1 406 UNP P77933 DPOL_THEKO 1 406 DBREF 7OM3 A 407 490 UNP P77933 DPOL_THEKO 767 850 DBREF 7OM3 A 491 774 UNP P77933 DPOL_THEKO 1388 1671 DBREF 7OM3 T 1 21 PDB 7OM3 7OM3 1 21 DBREF 7OM3 P 1 12 PDB 7OM3 7OM3 1 12 SEQADV 7OM3 ALA A 141 UNP P77933 ASP 141 ENGINEERED MUTATION SEQADV 7OM3 ALA A 143 UNP P77933 GLU 143 ENGINEERED MUTATION SEQRES 1 A 774 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 774 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 774 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 774 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 774 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 774 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 774 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 774 ASP VAL PRO ALA ILE ARG ASP LYS ILE ARG GLU HIS PRO SEQRES 9 A 774 ALA VAL ILE ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 774 LYS ARG TYR LEU ILE ASP LYS GLY LEU VAL PRO MET GLU SEQRES 11 A 774 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 774 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 774 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 774 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 774 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 774 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 774 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 774 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 774 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 774 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 774 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 774 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY GLN PRO SEQRES 23 A 774 LYS GLU LYS VAL TYR ALA GLU GLU ILE THR THR ALA TRP SEQRES 24 A 774 GLU THR GLY GLU ASN LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 774 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 774 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 774 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 774 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 774 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU LYS GLU LEU SEQRES 30 A 774 ALA ARG ARG ARG GLN SER TYR GLU GLY GLY TYR VAL LYS SEQRES 31 A 774 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 774 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 774 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 774 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE CYS SEQRES 35 A 774 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 774 LEU LEU GLU GLU ARG GLN LYS ILE LYS LYS LYS MET LYS SEQRES 37 A 774 ALA THR ILE ASP PRO ILE GLU ARG LYS LEU LEU ASP TYR SEQRES 38 A 774 ARG GLN ARG ALA ILE LYS ILE LEU ALA ASN SER TYR TYR SEQRES 39 A 774 GLY TYR TYR GLY TYR ALA ARG ALA ARG TRP TYR CYS LYS SEQRES 40 A 774 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 774 ILE THR MET THR ILE LYS GLU ILE GLU GLU LYS TYR GLY SEQRES 42 A 774 PHE LYS VAL ILE TYR SER ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 774 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 774 ALA MET GLU PHE LEU LYS TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 774 GLY ALA LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 774 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 774 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 774 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 774 ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL GLU SEQRES 50 A 774 LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 774 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 774 GLU GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 774 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 774 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 774 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 774 PRO PHE ASP GLU PHE ASP PRO THR LYS HIS LYS TYR ASP SEQRES 57 A 774 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 774 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 774 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU SER ALA SEQRES 60 A 774 TRP LEU LYS PRO LYS GLY THR SEQRES 1 T 21 DT DA DT DI DC DA DA DC DT DG DT DG DG SEQRES 2 T 21 DC DC DG DT DG DG DT DC SEQRES 1 P 12 DG DA DC DC DA DC DG DG DC DC DA DOC HET DOC P 12 30 HET PEG A 901 17 HET EDO A 902 10 HET EDO A 903 10 HET EDO A 904 10 HET BR A 905 1 HET BR A 906 1 HET GOL A 907 14 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM BR BROMIDE ION HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 4 PEG C4 H10 O3 FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 BR 2(BR 1-) FORMUL 10 GOL C3 H8 O3 FORMUL 11 HOH *382(H2 O) HELIX 1 AA1 ASP A 44 SER A 46 5 3 HELIX 2 AA2 ALA A 47 LYS A 53 1 7 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 ASN A 304 GLY A 338 1 35 HELIX 11 AB2 SER A 340 ARG A 346 1 7 HELIX 12 AB3 SER A 348 ARG A 364 1 17 HELIX 13 AB4 ASP A 373 ARG A 380 1 8 HELIX 14 AB5 SER A 407 HIS A 416 1 10 HELIX 15 AB6 GLY A 447 THR A 470 1 24 HELIX 16 AB7 ASP A 472 ASN A 491 1 20 HELIX 17 AB8 SER A 492 GLY A 498 1 7 HELIX 18 AB9 CYS A 506 GLY A 533 1 28 HELIX 19 AC1 ASP A 552 LEU A 571 1 20 HELIX 20 AC2 LEU A 608 ARG A 612 5 5 HELIX 21 AC3 SER A 616 LYS A 632 1 17 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 ARG 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 PHE A 19 N LEU A 3 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O ASP A 31 N ILE A 16 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 ALA A 56 ARG A 58 0 SHEET 2 AA3 2 THR A 61 VAL A 63 -1 O VAL A 63 N ALA A 56 SHEET 1 AA4 6 VAL A 181 VAL A 183 0 SHEET 2 AA4 6 GLY A 167 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ASP A 164 -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 SER 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 GLY A 395 PHE A 405 -1 N VAL A 401 O ALA A 546 SHEET 5 AA6 7 LEU A 577 THR A 590 -1 O TYR A 583 N ILE A 400 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 ARG 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 SSBOND 1 CYS A 428 CYS A 442 1555 1555 2.69 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.86 LINK O3' DA P 11 P DOC P 12 1555 1555 1.60 CRYST1 113.356 142.936 65.582 90.00 90.00 90.00 P 21 21 2 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 0.008822 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015248 0.00000