HEADER TRANSFERASE 06-SEP-17 5OXJ TITLE CRYSTAL STRUCTURE OF KLENTAQ MUTANT M747K IN A CLOSED TERNARY COMPLEX TITLE 2 WITH A O6-MEG:BENZITP BASE PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: MUTANT M747K; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA PRIMER; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA TEMPLATE; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; 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 DNA POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,K.DIEDERICHS,A.MARX REVDAT 3 17-JAN-24 5OXJ 1 LINK REVDAT 2 06-DEC-17 5OXJ 1 JRNL REVDAT 1 29-NOV-17 5OXJ 0 JRNL AUTH K.BETZ,A.NILFOROUSHAN,L.A.WYSS,K.DIEDERICHS,S.J.STURLA, JRNL AUTH 2 A.MARX JRNL TITL STRUCTURAL BASIS FOR THE SELECTIVE INCORPORATION OF AN JRNL TITL 2 ARTIFICIAL NUCLEOTIDE OPPOSITE A DNA ADDUCT BY A DNA JRNL TITL 3 POLYMERASE. JRNL REF CHEM. COMMUN. (CAMB.) V. 53 12704 2017 JRNL REFN ESSN 1364-548X JRNL PMID 29136072 JRNL DOI 10.1039/C7CC07173F REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2815: ???) 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) : 47.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 81358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4101 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 47.3619 - 6.1401 0.98 2613 154 0.1402 0.1979 REMARK 3 2 6.1401 - 4.8752 1.00 2684 147 0.1404 0.2234 REMARK 3 3 4.8752 - 4.2594 1.00 2712 124 0.1211 0.1813 REMARK 3 4 4.2594 - 3.8701 1.00 2657 173 0.1279 0.1759 REMARK 3 5 3.8701 - 3.5928 0.97 2557 165 0.1620 0.2240 REMARK 3 6 3.5928 - 3.3811 1.00 2646 151 0.1773 0.2332 REMARK 3 7 3.3811 - 3.2118 1.00 2704 134 0.2058 0.2664 REMARK 3 8 3.2118 - 3.0720 1.00 2705 150 0.2192 0.3015 REMARK 3 9 3.0720 - 2.9538 1.00 2651 133 0.2532 0.3894 REMARK 3 10 2.9538 - 2.8518 1.00 2701 152 0.2617 0.3025 REMARK 3 11 2.8518 - 2.7627 1.00 2673 148 0.2626 0.3385 REMARK 3 12 2.7627 - 2.6837 1.00 2674 141 0.2485 0.3150 REMARK 3 13 2.6837 - 2.6131 1.00 2653 160 0.2493 0.3370 REMARK 3 14 2.6131 - 2.5493 0.98 2627 130 0.2444 0.2560 REMARK 3 15 2.5493 - 2.4914 0.99 2580 166 0.2519 0.3283 REMARK 3 16 2.4914 - 2.4384 1.00 2749 138 0.2468 0.3161 REMARK 3 17 2.4384 - 2.3896 1.00 2690 131 0.2577 0.3134 REMARK 3 18 2.3896 - 2.3445 1.00 2749 116 0.2737 0.3984 REMARK 3 19 2.3445 - 2.3026 1.00 2654 131 0.2871 0.3193 REMARK 3 20 2.3026 - 2.2636 1.00 2669 143 0.2843 0.3310 REMARK 3 21 2.2636 - 2.2271 1.00 2647 133 0.2997 0.3496 REMARK 3 22 2.2271 - 2.1928 0.99 2675 115 0.3009 0.3347 REMARK 3 23 2.1928 - 2.1606 1.00 2696 143 0.2940 0.3377 REMARK 3 24 2.1606 - 2.1301 0.99 2707 122 0.3055 0.3662 REMARK 3 25 2.1301 - 2.1013 0.99 2626 127 0.3303 0.3876 REMARK 3 26 2.1013 - 2.0741 0.99 2707 132 0.3461 0.3473 REMARK 3 27 2.0741 - 2.0481 0.99 2625 141 0.3715 0.4004 REMARK 3 28 2.0481 - 2.0235 1.00 2633 149 0.3754 0.3667 REMARK 3 29 2.0235 - 1.9999 0.96 2593 152 0.4003 0.4477 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.430 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 5000 REMARK 3 ANGLE : 0.958 6886 REMARK 3 CHIRALITY : 0.051 754 REMARK 3 PLANARITY : 0.006 840 REMARK 3 DIHEDRAL : 16.237 2963 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 294 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4246 -41.0541 -18.2248 REMARK 3 T TENSOR REMARK 3 T11: 0.3411 T22: 0.3902 REMARK 3 T33: 0.5521 T12: -0.1157 REMARK 3 T13: 0.0620 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.5035 L22: 0.3683 REMARK 3 L33: 0.7461 L12: -0.1625 REMARK 3 L13: 0.0940 L23: 0.5061 REMARK 3 S TENSOR REMARK 3 S11: 0.0178 S12: -0.0379 S13: -0.2613 REMARK 3 S21: -0.1927 S22: 0.0455 S23: -0.2675 REMARK 3 S31: 0.1090 S32: -0.0689 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 632 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.0395 -12.5124 -1.5027 REMARK 3 T TENSOR REMARK 3 T11: 0.4461 T22: 0.3080 REMARK 3 T33: 0.3278 T12: 0.0482 REMARK 3 T13: 0.0253 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 1.0999 L22: 0.8058 REMARK 3 L33: 1.0837 L12: 0.9416 REMARK 3 L13: -0.2078 L23: -0.4697 REMARK 3 S TENSOR REMARK 3 S11: 0.0743 S12: 0.0753 S13: 0.0692 REMARK 3 S21: 0.0939 S22: -0.0186 S23: -0.0062 REMARK 3 S31: -0.5226 S32: -0.3218 S33: 0.0178 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 633 THROUGH 681 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8823 -12.1958 -3.7883 REMARK 3 T TENSOR REMARK 3 T11: 1.0411 T22: 0.9515 REMARK 3 T33: 0.8529 T12: 0.2861 REMARK 3 T13: -0.0909 T23: 0.0448 REMARK 3 L TENSOR REMARK 3 L11: 0.0438 L22: 0.0608 REMARK 3 L33: 0.0027 L12: -0.0854 REMARK 3 L13: 0.0244 L23: -0.0300 REMARK 3 S TENSOR REMARK 3 S11: -0.1252 S12: -0.1312 S13: 0.3334 REMARK 3 S21: -0.0161 S22: 0.4678 S23: 0.2103 REMARK 3 S31: 0.0916 S32: 0.2500 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 682 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2322 -24.4733 -12.7038 REMARK 3 T TENSOR REMARK 3 T11: 0.3034 T22: 0.6280 REMARK 3 T33: 0.3037 T12: -0.0133 REMARK 3 T13: -0.0168 T23: 0.0450 REMARK 3 L TENSOR REMARK 3 L11: 0.4494 L22: 0.8842 REMARK 3 L33: 0.9703 L12: 0.2084 REMARK 3 L13: 0.2651 L23: 0.0150 REMARK 3 S TENSOR REMARK 3 S11: -0.1177 S12: 0.1025 S13: 0.0057 REMARK 3 S21: -0.1324 S22: 0.2285 S23: 0.0655 REMARK 3 S31: -0.3287 S32: -0.6508 S33: 0.0052 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1755 -23.5379 5.1394 REMARK 3 T TENSOR REMARK 3 T11: 0.2418 T22: 0.5374 REMARK 3 T33: 0.4848 T12: 0.0523 REMARK 3 T13: -0.0002 T23: 0.1118 REMARK 3 L TENSOR REMARK 3 L11: 0.0198 L22: 0.3181 REMARK 3 L33: 0.4830 L12: 0.1476 REMARK 3 L13: -0.1468 L23: -0.3953 REMARK 3 S TENSOR REMARK 3 S11: 0.0027 S12: 0.3121 S13: -0.2026 REMARK 3 S21: 0.4740 S22: -0.4172 S23: -0.0460 REMARK 3 S31: -0.4763 S32: 0.2580 S33: -0.1281 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.8724 -23.1455 6.3390 REMARK 3 T TENSOR REMARK 3 T11: 0.3560 T22: 0.5717 REMARK 3 T33: 0.4151 T12: 0.0480 REMARK 3 T13: -0.0092 T23: 0.0830 REMARK 3 L TENSOR REMARK 3 L11: 0.1422 L22: 0.4740 REMARK 3 L33: 0.4641 L12: 0.1925 REMARK 3 L13: -0.1578 L23: 0.2960 REMARK 3 S TENSOR REMARK 3 S11: -0.1755 S12: -0.4005 S13: -0.3304 REMARK 3 S21: 0.2332 S22: 0.0688 S23: -0.0672 REMARK 3 S31: -0.1670 S32: -0.3352 S33: -0.0001 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 5OXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006479. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-16 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) : 0.999987 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81385 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.349 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7100 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.940 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: 3M8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG3350 + 0.1M MG(OAC)2 + 0.1M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.21200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.42400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.42400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.21200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 PHE A 647 REMARK 465 GLY A 648 REMARK 465 VAL A 649 REMARK 465 PRO A 650 REMARK 465 ARG A 651 REMARK 465 GLU A 652 REMARK 465 ALA A 653 REMARK 465 VAL A 654 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 MN MN A 901 H17 NZI A 903 1.45 REMARK 500 OE1 GLU A 462 O HOH A 1001 2.09 REMARK 500 O GLU A 303 NH1 ARG A 328 2.16 REMARK 500 OD1 ASP A 320 OH TYR A 339 2.17 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 DA B 105 O3' DA B 105 C3' -0.042 REMARK 500 DT C 212 O3' DT C 212 C3' -0.038 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 B 108 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DDG B 112 O3' - P - O5' ANGL. DEV. = 13.3 DEGREES REMARK 500 DDG B 112 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 DDG B 112 O3' - P - OP1 ANGL. DEV. = -22.0 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 328 138.87 -173.72 REMARK 500 VAL A 433 -66.24 -122.41 REMARK 500 ALA A 521 0.07 -67.97 REMARK 500 HIS A 526 145.70 171.63 REMARK 500 TYR A 545 -59.73 -125.62 REMARK 500 VAL A 586 -15.80 -163.23 REMARK 500 TYR A 671 35.09 -98.36 REMARK 500 HIS A 784 -56.86 72.56 REMARK 500 TYR A 811 91.50 -165.90 REMARK 500 ALA A 814 -6.61 -58.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 416 DISTANCE = 6.90 ANGSTROMS 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 906 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 462 OE1 REMARK 620 2 GLU A 825 OE1 64.7 REMARK 620 3 GLU A 825 OE2 63.4 2.6 REMARK 620 4 HOH A1001 O 46.4 103.5 103.2 REMARK 620 5 HOH A1071 O 108.3 158.0 155.4 82.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 78.4 REMARK 620 3 ASP A 785 OD2 108.1 88.1 REMARK 620 4 NZI A 903 O4 94.3 172.6 92.8 REMARK 620 5 NZI A 903 O7 163.5 97.0 87.4 90.4 REMARK 620 6 NZI A 903 O11 70.0 100.9 170.0 77.8 95.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 902 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 NZI A 903 O4 111.6 REMARK 620 3 HOH A1004 O 83.7 135.8 REMARK 620 4 HOH A1016 O 87.0 67.5 156.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 305 O REMARK 620 2 HOH B 306 O 79.9 REMARK 620 3 HOH B 309 O 87.6 78.9 REMARK 620 4 HOH B 311 O 142.1 65.7 71.2 REMARK 620 5 HOH C 415 O 98.0 87.6 164.3 96.1 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NZI A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 301 DBREF 5OXJ A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5OXJ B 101 112 PDB 5OXJ 5OXJ 101 112 DBREF 5OXJ C 201 216 PDB 5OXJ 5OXJ 201 216 SEQADV 5OXJ LYS A 747 UNP P19821 MET 747 ENGINEERED MUTATION SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG LYS SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DDG SEQRES 1 C 16 DA DA DA 6OG DC DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET DDG B 112 21 HET 6OG C 204 38 HET MN A 901 1 HET MN A 902 1 HET NZI A 903 47 HET ACT A 904 7 HET ACT A 905 7 HET MG A 906 1 HET MG B 201 1 HET ACT C 301 7 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NZI [(2~{R},3~{S},5~{R})-3-OXIDANYL-5-(2-OXIDANYLIDENE- HETNAM 2 NZI 3~{H}-BENZIMIDAZOL-1-YL)OXOLAN-2-YL]METHYL HETNAM 3 NZI [OXIDANYL(PHOSPHONOOXY)PHOSPHORYL] HYDROGEN PHOSPHATE HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 3 6OG C11 H16 N5 O7 P FORMUL 4 MN 2(MN 2+) FORMUL 6 NZI C12 H17 N2 O13 P3 FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 9 MG 2(MG 2+) FORMUL 12 HOH *98(H2 O) HELIX 1 AA1 GLU A 337 ARG A 343 1 7 HELIX 2 AA2 LEU A 352 GLU A 363 1 12 HELIX 3 AA3 ASP A 372 ASP A 381 1 10 HELIX 4 AA4 THR A 386 GLY A 395 1 10 HELIX 5 AA5 GLU A 401 GLU A 421 1 21 HELIX 6 AA6 GLU A 423 VAL A 433 1 11 HELIX 7 AA7 VAL A 433 GLY A 448 1 16 HELIX 8 AA8 ASP A 452 ALA A 478 1 27 HELIX 9 AA9 SER A 486 ASP A 496 1 11 HELIX 10 AB1 SER A 515 ALA A 521 1 7 HELIX 11 AB2 HIS A 526 TYR A 545 1 20 HELIX 12 AB3 PRO A 548 ILE A 553 5 6 HELIX 13 AB4 THR A 588 ARG A 596 1 9 HELIX 14 AB5 GLN A 613 GLY A 624 1 12 HELIX 15 AB6 ASP A 625 GLU A 634 1 10 HELIX 16 AB7 THR A 640 MET A 646 1 7 HELIX 17 AB8 PRO A 656 TYR A 671 1 16 HELIX 18 AB9 SER A 674 LEU A 682 1 9 HELIX 19 AC1 PRO A 685 SER A 699 1 15 HELIX 20 AC2 PRO A 701 GLY A 718 1 18 HELIX 21 AC3 PRO A 731 ALA A 735 5 5 HELIX 22 AC4 VAL A 737 MET A 775 1 39 HELIX 23 AC5 ARG A 795 GLY A 809 1 15 HELIX 24 AC6 LEU A 828 GLU A 832 5 5 SHEET 1 AA1 4 GLU A 295 GLU A 296 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N GLU A 295 SHEET 3 AA1 4 LEU A 321 ALA A 327 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N LEU A 609 O LEU A 787 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DDG B 112 1555 1555 1.56 LINK O3' DA C 203 P 6OG C 204 1555 1555 1.61 LINK O3' 6OG C 204 P DC C 205 1555 1555 1.59 LINK OE1 GLU A 462 MG MG A 906 1555 1555 2.30 LINK OD1 ASP A 610 MN MN A 901 1555 1555 2.47 LINK OD2 ASP A 610 MN MN A 902 1555 1555 2.14 LINK O TYR A 611 MN MN A 901 1555 1555 2.09 LINK OD2 ASP A 785 MN MN A 901 1555 1555 2.21 LINK OE1 GLU A 825 MG MG A 906 1555 5554 2.81 LINK OE2 GLU A 825 MG MG A 906 1555 5554 2.04 LINK MN MN A 901 O4 NZI A 903 1555 1555 2.56 LINK MN MN A 901 O7 NZI A 903 1555 1555 2.44 LINK MN MN A 901 O11 NZI A 903 1555 1555 2.10 LINK MN MN A 902 O4 NZI A 903 1555 1555 2.03 LINK MN MN A 902 O HOH A1004 1555 1555 2.22 LINK MN MN A 902 O HOH A1016 1555 1555 2.57 LINK MG MG A 906 O HOH A1001 1555 1555 2.85 LINK MG MG A 906 O HOH A1071 1555 5554 2.51 LINK MG MG B 201 O HOH B 305 1555 1555 2.14 LINK MG MG B 201 O HOH B 306 1555 1555 2.17 LINK MG MG B 201 O HOH B 309 1555 1555 2.07 LINK MG MG B 201 O HOH B 311 1555 1555 2.47 LINK MG MG B 201 O HOH C 415 1555 1555 2.10 CISPEP 1 TRP A 299 PRO A 300 0 8.07 CISPEP 2 ASP A 578 PRO A 579 0 -3.18 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MN A 902 SITE 2 AC1 5 NZI A 903 SITE 1 AC2 7 ASP A 610 ASP A 785 GLU A 786 MN A 901 SITE 2 AC2 7 NZI A 903 HOH A1004 HOH A1016 SITE 1 AC3 18 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 2 AC3 18 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 18 ARG A 659 LYS A 663 PHE A 667 ASP A 785 SITE 4 AC3 18 MN A 901 MN A 902 HOH A1005 HOH A1016 SITE 5 AC3 18 DDG B 112 6OG C 204 SITE 1 AC4 2 HIS A 443 GLU A 773 SITE 1 AC5 2 ARG A 313 TRP A 318 SITE 1 AC6 4 GLU A 462 GLU A 825 HOH A1001 HOH A1071 SITE 1 AC7 5 HOH B 305 HOH B 306 HOH B 309 HOH B 311 SITE 2 AC7 5 HOH C 415 SITE 1 AC8 2 DG C 213 DG C 214 CRYST1 109.347 109.347 90.636 90.00 90.00 120.00 P 31 2 1 6 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 0.009145 0.005280 0.000000 0.00000 SCALE2 0.000000 0.010560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011033 0.00000