HEADER TRANSFERASE 01-AUG-17 5OMQ TITLE TERNARY COMPLEX OF 9N DNA POLYMERASE IN THE REPLICATIVE STATE WITH TITLE 2 THREE 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. (STRAIN 9ON-7); SOURCE 3 ORGANISM_TAXID: 103799; SOURCE 4 STRAIN: 9ON-7; SOURCE 5 GENE: POL, POLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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 TERNARY COMPLEX, DNA POLYMERASE, TRIPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,A.MARX,K.DIEDERICHS REVDAT 2 17-JAN-24 5OMQ 1 LINK REVDAT 1 20-DEC-17 5OMQ 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 96987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 4955 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 46.8496 - 6.8273 1.00 3064 178 0.1366 0.1833 REMARK 3 2 6.8273 - 5.4217 0.99 3096 128 0.1561 0.2136 REMARK 3 3 5.4217 - 4.7371 1.00 3067 175 0.1248 0.1752 REMARK 3 4 4.7371 - 4.3043 1.00 3089 159 0.1260 0.1624 REMARK 3 5 4.3043 - 3.9959 0.99 3039 169 0.1349 0.1611 REMARK 3 6 3.9959 - 3.7605 0.99 3067 166 0.1583 0.2518 REMARK 3 7 3.7605 - 3.5722 1.00 3079 166 0.1751 0.2459 REMARK 3 8 3.5722 - 3.4168 1.00 3059 199 0.1937 0.2547 REMARK 3 9 3.4168 - 3.2853 1.00 3078 142 0.2061 0.2769 REMARK 3 10 3.2853 - 3.1719 1.00 3046 174 0.1991 0.2494 REMARK 3 11 3.1719 - 3.0728 1.00 3099 170 0.2165 0.3146 REMARK 3 12 3.0728 - 2.9849 1.00 3123 140 0.2089 0.2596 REMARK 3 13 2.9849 - 2.9064 1.00 3011 185 0.2163 0.3080 REMARK 3 14 2.9064 - 2.8355 1.00 3073 170 0.2453 0.3313 REMARK 3 15 2.8355 - 2.7710 1.00 3090 140 0.2559 0.3061 REMARK 3 16 2.7710 - 2.7121 1.00 3093 196 0.2484 0.3644 REMARK 3 17 2.7121 - 2.6578 1.00 3026 184 0.2558 0.3115 REMARK 3 18 2.6578 - 2.6077 1.00 3087 151 0.2524 0.3162 REMARK 3 19 2.6077 - 2.5611 1.00 3051 202 0.2660 0.3392 REMARK 3 20 2.5611 - 2.5177 0.99 3042 188 0.2674 0.3093 REMARK 3 21 2.5177 - 2.4771 1.00 3040 157 0.2794 0.3357 REMARK 3 22 2.4771 - 2.4390 1.00 3141 147 0.2908 0.3069 REMARK 3 23 2.4390 - 2.4031 1.00 3028 171 0.2961 0.3539 REMARK 3 24 2.4031 - 2.3692 1.00 3124 155 0.3074 0.3685 REMARK 3 25 2.3692 - 2.3372 1.00 3082 162 0.3126 0.3534 REMARK 3 26 2.3372 - 2.3069 1.00 3081 155 0.3268 0.3379 REMARK 3 27 2.3069 - 2.2780 1.00 3098 159 0.3445 0.3661 REMARK 3 28 2.2780 - 2.2506 1.00 3044 164 0.3992 0.4081 REMARK 3 29 2.2506 - 2.2244 0.99 3072 163 0.4637 0.4713 REMARK 3 30 2.2244 - 2.1994 0.95 2943 140 0.4068 0.4630 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.940 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 7025 REMARK 3 ANGLE : 0.934 9592 REMARK 3 CHIRALITY : 0.052 1023 REMARK 3 PLANARITY : 0.006 1151 REMARK 3 DIHEDRAL : 14.165 4164 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): 109.9723 95.2711 3.5534 REMARK 3 T TENSOR REMARK 3 T11: 0.3497 T22: 0.6807 REMARK 3 T33: 0.4226 T12: 0.0614 REMARK 3 T13: 0.0400 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 1.4268 L22: 1.5557 REMARK 3 L33: 1.7963 L12: 1.1455 REMARK 3 L13: 0.8299 L23: 0.6714 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: -0.0368 S13: -0.0800 REMARK 3 S21: 0.0046 S22: -0.0801 S23: -0.2450 REMARK 3 S31: 0.1517 S32: 0.2549 S33: 0.0080 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 109.7977 106.5329 17.5489 REMARK 3 T TENSOR REMARK 3 T11: 0.3942 T22: 0.7343 REMARK 3 T33: 0.4227 T12: -0.0207 REMARK 3 T13: -0.0581 T23: 0.0580 REMARK 3 L TENSOR REMARK 3 L11: 2.6375 L22: 2.7563 REMARK 3 L33: 0.8577 L12: 1.9112 REMARK 3 L13: -0.4830 L23: -0.1521 REMARK 3 S TENSOR REMARK 3 S11: 0.1127 S12: -0.3348 S13: 0.2457 REMARK 3 S21: 0.2111 S22: -0.1979 S23: 0.0269 REMARK 3 S31: -0.1144 S32: 0.2233 S33: 0.0932 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 365 THROUGH 552 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.7262 93.1512 21.2165 REMARK 3 T TENSOR REMARK 3 T11: 0.3956 T22: 0.4334 REMARK 3 T33: 0.3953 T12: -0.0701 REMARK 3 T13: 0.0044 T23: 0.0725 REMARK 3 L TENSOR REMARK 3 L11: 2.0783 L22: 0.4238 REMARK 3 L33: 3.9539 L12: -0.3937 REMARK 3 L13: -1.2308 L23: 0.6922 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: 0.0289 S13: -0.1902 REMARK 3 S21: 0.0879 S22: -0.0661 S23: 0.0570 REMARK 3 S31: 0.1467 S32: -0.2043 S33: 0.1622 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 553 THROUGH 758 ) REMARK 3 ORIGIN FOR THE GROUP (A): 85.4489 119.9088 31.1100 REMARK 3 T TENSOR REMARK 3 T11: 0.3313 T22: 0.6363 REMARK 3 T33: 0.4166 T12: 0.0168 REMARK 3 T13: -0.0582 T23: -0.0423 REMARK 3 L TENSOR REMARK 3 L11: 1.2967 L22: 2.8230 REMARK 3 L33: 1.3903 L12: 0.4835 REMARK 3 L13: -0.1877 L23: -0.4356 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: -0.2253 S13: 0.2348 REMARK 3 S21: 0.2417 S22: 0.0343 S23: -0.3477 REMARK 3 S31: -0.2183 S32: 0.1465 S33: -0.0080 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 3 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.8997 117.5482 15.2602 REMARK 3 T TENSOR REMARK 3 T11: 0.3250 T22: 0.5984 REMARK 3 T33: 0.3477 T12: 0.0240 REMARK 3 T13: -0.0297 T23: 0.0738 REMARK 3 L TENSOR REMARK 3 L11: 0.0072 L22: 9.1269 REMARK 3 L33: 0.4622 L12: -0.6270 REMARK 3 L13: 0.0232 L23: -1.6942 REMARK 3 S TENSOR REMARK 3 S11: 0.1274 S12: 0.2132 S13: 0.1212 REMARK 3 S21: -0.1851 S22: -0.0448 S23: -0.0525 REMARK 3 S31: -0.0645 S32: -0.1377 S33: -0.1016 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.6375 119.5894 16.9496 REMARK 3 T TENSOR REMARK 3 T11: 0.4274 T22: 0.6483 REMARK 3 T33: 0.4350 T12: 0.0119 REMARK 3 T13: -0.0452 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.5334 L22: 3.7770 REMARK 3 L33: 1.6028 L12: -3.1427 REMARK 3 L13: 0.8858 L23: -1.1379 REMARK 3 S TENSOR REMARK 3 S11: 0.2281 S12: 0.5518 S13: -0.0813 REMARK 3 S21: -0.3061 S22: -0.3051 S23: 0.1484 REMARK 3 S31: -0.1325 S32: -0.0414 S33: 0.1087 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 5OMQ 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_1200005429. 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) : 0.999975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97025 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.199 REMARK 200 RESOLUTION RANGE LOW (A) : 46.839 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 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 : 0.920 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: 4K8X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5, REMARK 280 6% ISOPROPANOL, 36% PEG 550 MME, VAPOR DIFFUSION, SITTING 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 33.39650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.10250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.83900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.10250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.39650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.83900 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: 6710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 465 DA T 2 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 OD2 ASP A 44 OG SER A 46 1.88 REMARK 500 NH1 ARG A 310 OE2 GLU A 314 2.10 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 DG T 5 O3' DG T 5 C3' -0.044 REMARK 500 DC P 4 O3' DC P 4 C3' -0.039 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG T 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC P 4 O4' - C1' - N1 ANGL. DEV. = 2.2 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 MET A 129 36.19 76.13 REMARK 500 ASN A 424 61.76 35.29 REMARK 500 GLU A 426 -141.02 42.48 REMARK 500 GLU A 436 -54.92 69.78 REMARK 500 PHE A 448 -71.02 -51.88 REMARK 500 TRP A 504 48.86 -87.02 REMARK 500 CYS A 506 87.70 -167.56 REMARK 500 THR A 541 -64.82 66.34 REMARK 500 LYS A 592 -9.89 71.68 REMARK 500 ASP A 718 -16.11 -48.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD2 REMARK 620 2 ASP A 542 OD1 105.0 REMARK 620 3 DTP A 806 O2A 102.2 85.8 REMARK 620 4 HOH A 951 O 78.5 171.0 85.3 REMARK 620 5 HOH A 960 O 96.7 103.2 156.2 84.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 804 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD1 REMARK 620 2 GLU A 580 OE1 109.4 REMARK 620 3 DTP A 806 O3G 77.7 164.7 REMARK 620 4 HOH A 923 O 90.1 92.1 101.6 REMARK 620 5 HOH A 934 O 168.9 77.5 93.6 98.5 REMARK 620 6 HOH A 936 O 88.2 83.5 83.2 174.5 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 805 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD1 REMARK 620 2 PHE A 405 O 80.7 REMARK 620 3 ASP A 542 OD2 95.5 83.7 REMARK 620 4 DTP A 806 O3G 85.4 94.0 177.3 REMARK 620 5 DTP A 806 O2B 167.1 91.1 93.4 85.3 REMARK 620 6 DTP A 806 O2A 101.9 174.9 100.3 81.9 85.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTP A 806 DBREF 5OMQ A 1 775 UNP Q56366 DPOL_THES9 1 775 DBREF 5OMQ T 1 16 PDB 5OMQ 5OMQ 1 16 DBREF 5OMQ P 1 10 PDB 5OMQ 5OMQ 1 10 SEQADV 5OMQ ALA A 141 UNP Q56366 ASP 141 ENGINEERED MUTATION SEQADV 5OMQ 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 GOL A 801 6 HET PGE A 802 10 HET MG A 803 1 HET MG A 804 1 HET MN A 805 1 HET DTP A 806 42 HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETNAM MG MAGNESIUM ION HETNAM MN MANGANESE (II) ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 PGE C6 H14 O4 FORMUL 6 MG 2(MG 2+) FORMUL 8 MN MN 2+ FORMUL 9 DTP C10 H16 N5 O12 P3 FORMUL 10 HOH *90(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 ALA A 102 1 12 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 GLU A 300 1 10 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 379 1 7 HELIX 14 AB5 SER A 407 HIS A 416 1 10 HELIX 15 AB6 ILE A 449 THR A 470 1 22 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 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 ALA A 688 1 12 HELIX 26 AC8 ASP A 718 PHE A 720 5 3 HELIX 27 AC9 ASP A 728 GLN A 736 1 9 HELIX 28 AD1 GLN A 736 LYS A 746 1 11 HELIX 29 AD2 ALA A 747 GLY A 749 5 3 HELIX 30 AD3 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 ALA A 40 O TRP A 83 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 139 O ALA A 163 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 ILE A 256 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 ILE A 597 -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 OD2 ASP A 404 MG MG A 803 1555 1555 2.12 LINK OD1 ASP A 404 MG MG A 804 1555 1555 2.56 LINK OD1 ASP A 404 MN A MN A 805 1555 1555 2.14 LINK O PHE A 405 MN A MN A 805 1555 1555 2.06 LINK OD1 ASP A 542 MG MG A 803 1555 1555 2.17 LINK OD2 ASP A 542 MN A MN A 805 1555 1555 2.23 LINK OE1 GLU A 580 MG MG A 804 1555 1555 2.42 LINK MG MG A 803 O2A DTP A 806 1555 1555 2.46 LINK MG MG A 803 O HOH A 951 1555 1555 2.56 LINK MG MG A 803 O HOH A 960 1555 1555 2.30 LINK MG MG A 804 O3G DTP A 806 1555 1555 2.18 LINK MG MG A 804 O HOH A 923 1555 1555 1.96 LINK MG MG A 804 O HOH A 934 1555 1555 2.34 LINK MG MG A 804 O HOH A 936 1555 1555 2.13 LINK MN A MN A 805 O3G DTP A 806 1555 1555 2.26 LINK MN A MN A 805 O2B DTP A 806 1555 1555 2.12 LINK MN A MN A 805 O2A DTP A 806 1555 1555 2.24 SITE 1 AC1 6 TYR A 402 HIS A 545 TYR A 583 TYR A 594 SITE 2 AC1 6 ARG A 606 DC P 12 SITE 1 AC2 7 ASP A 404 ASP A 542 MN A 805 DTP A 806 SITE 2 AC2 7 HOH A 951 HOH A 960 DC P 12 SITE 1 AC3 7 ASP A 404 GLU A 580 MN A 805 DTP A 806 SITE 2 AC3 7 HOH A 923 HOH A 934 HOH A 936 SITE 1 AC4 6 ASP A 404 PHE A 405 ASP A 542 MG A 803 SITE 2 AC4 6 MG A 804 DTP A 806 SITE 1 AC5 18 ASP A 404 PHE A 405 ARG A 406 SER A 407 SITE 2 AC5 18 LEU A 408 TYR A 409 ARG A 460 LYS A 487 SITE 3 AC5 18 ASN A 491 ASP A 542 MG A 803 MG A 804 SITE 4 AC5 18 MN A 805 HOH A 934 HOH A 936 DC P 12 SITE 5 AC5 18 DT T 4 DG T 5 CRYST1 66.793 93.678 158.205 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 0.014972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006321 0.00000