HEADER DNA BINDING PROTEIN 23-MAR-22 7UFX TITLE ISORETICULAR, INTERPENETRATING CO-CRYSTAL OF REPLICATION INITIATOR TITLE 2 PROTEIN REPE54 AND SCAFFOLD-INSERT DUPLEXES (21MER AND 10MER) TITLE 3 CONTAINING THE COGNATE REPE54 SEQUENCE AND AN ADDITIONAL G-C RICH TITLE 4 SEQUENCE, RESPECTIVELY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(A*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*A)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(A*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)- COMPND 10 3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: REPLICATION INITIATION PROTEIN; COMPND 15 CHAIN: C; COMPND 16 SYNONYM: PROTEIN E,PROTEIN REP,PROTEIN F4; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: DNA (5'-D(A*GP*AP*CP*GP*GP*CP*CP*CP*GP*G)-3'); COMPND 21 CHAIN: E; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 5; COMPND 24 MOLECULE: DNA (5'-D(A*GP*TP*CP*CP*GP*GP*GP*CP*CP*G)-3'); COMPND 25 CHAIN: F; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 11 ORGANISM_TAXID: 83333; SOURCE 12 STRAIN: K12; SOURCE 13 GENE: REPE, E, REP, ECOK12F045; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 19 ORGANISM_TAXID: 562; SOURCE 20 MOL_ID: 5; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 23 ORGANISM_TAXID: 562 KEYWDS REPLICATION INITIATOR REPE COMPLEX CO-CRYSTAL, DNA BINDING PROTEIN- KEYWDS 2 DNA COMPLEX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.WARD,E.T.SHIELDS,C.D.SNOW REVDAT 3 01-NOV-23 7UFX 1 JRNL REVDAT 2 25-OCT-23 7UFX 1 REMARK REVDAT 1 29-MAR-23 7UFX 0 JRNL AUTH A.R.ORUN,E.T.SHIELDS,S.DMYTRIW,A.VAJAPAYAJULA,C.K.SLAUGHTER, JRNL AUTH 2 C.D.SNOW JRNL TITL MODULAR PROTEIN-DNA COCRYSTALS AS PRECISE, PROGRAMMABLE JRNL TITL 2 ASSEMBLY SCAFFOLDS. JRNL REF ACS NANO V. 17 13110 2023 JRNL REFN ESSN 1936-086X JRNL PMID 37407546 JRNL DOI 10.1021/ACSNANO.2C07282 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 68 352 2012 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.LIEBSCHNER,P.V.AFONINE,M.L.BAKER,G.BUNKOCZI,V.B.CHEN, REMARK 1 AUTH 2 T.I.CROLL,B.HINTZE,L.W.HUNG,S.JAIN,A.J.MCCOY,N.W.MORIARTY, REMARK 1 AUTH 3 R.D.OEFFNER,B.K.POON,M.G.PRISANT,R.J.READ,J.S.RICHARDSON, REMARK 1 AUTH 4 D.C.RICHARDSON,M.D.SAMMITO,O.V.SOBOLEV,D.H.STOCKWELL, REMARK 1 AUTH 5 T.C.TERWILLIGER,A.G.URZHUMTSEV,L.L.VIDEAU,C.J.WILLIAMS, REMARK 1 AUTH 6 P.D.ADAMS REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX. REMARK 1 REF ACTA CRYSTALLOGR D STRUCT V. 75 861 2019 REMARK 1 REF 2 BIOL REMARK 1 REFN ISSN 2059-7983 REMARK 1 PMID 31588918 REMARK 1 DOI 10.1107/S2059798319011471 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1665 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 39.0000 - 6.4000 0.98 1328 150 0.1907 0.1904 REMARK 3 2 6.4000 - 5.0800 1.00 1274 144 0.1812 0.2103 REMARK 3 3 5.0800 - 4.4400 1.00 1271 140 0.1575 0.1909 REMARK 3 4 4.4400 - 4.0400 1.00 1258 142 0.1622 0.2036 REMARK 3 5 4.0400 - 3.7500 1.00 1253 133 0.1799 0.2363 REMARK 3 6 3.7500 - 3.5300 1.00 1273 141 0.1824 0.2458 REMARK 3 7 3.5300 - 3.3500 0.99 1237 135 0.1918 0.2116 REMARK 3 8 3.3500 - 3.2100 0.99 1227 140 0.2041 0.2358 REMARK 3 9 3.2000 - 3.0800 1.00 1237 129 0.2443 0.2916 REMARK 3 10 3.0800 - 2.9800 1.00 1224 144 0.2912 0.3693 REMARK 3 11 2.9800 - 2.8800 1.00 1238 133 0.3564 0.4165 REMARK 3 12 2.8800 - 2.8000 1.00 1244 134 0.4020 0.4509 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) : 0.454 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.83 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 : 0.005 3255 REMARK 3 ANGLE : 0.906 4666 REMARK 3 CHIRALITY : 0.059 507 REMARK 3 PLANARITY : 0.007 379 REMARK 3 DIHEDRAL : 27.338 858 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3186 -13.3828 -5.1742 REMARK 3 T TENSOR REMARK 3 T11: 0.7233 T22: 0.5551 REMARK 3 T33: 0.9507 T12: -0.0023 REMARK 3 T13: 0.2048 T23: -0.3774 REMARK 3 L TENSOR REMARK 3 L11: 3.7324 L22: 2.2014 REMARK 3 L33: 7.2238 L12: -1.5690 REMARK 3 L13: -3.6423 L23: 1.4414 REMARK 3 S TENSOR REMARK 3 S11: -0.1396 S12: -0.0866 S13: 0.3397 REMARK 3 S21: -0.0140 S22: 0.3176 S23: -1.0788 REMARK 3 S31: -0.5244 S32: -0.2747 S33: -0.0879 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2791 -33.7921 -28.5164 REMARK 3 T TENSOR REMARK 3 T11: 1.1982 T22: 1.1875 REMARK 3 T33: 0.7460 T12: 0.2051 REMARK 3 T13: 0.8350 T23: -0.7702 REMARK 3 L TENSOR REMARK 3 L11: 0.4900 L22: 0.2298 REMARK 3 L33: 1.4258 L12: -0.0173 REMARK 3 L13: -0.1603 L23: 0.0776 REMARK 3 S TENSOR REMARK 3 S11: 0.2716 S12: 0.8015 S13: -0.1819 REMARK 3 S21: -0.6297 S22: -0.2926 S23: -0.4896 REMARK 3 S31: 0.3623 S32: 0.4442 S33: -0.1382 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 22 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0410 -37.2462 -30.4959 REMARK 3 T TENSOR REMARK 3 T11: 1.2640 T22: 0.8482 REMARK 3 T33: 0.9762 T12: 0.0978 REMARK 3 T13: 0.6404 T23: -0.6566 REMARK 3 L TENSOR REMARK 3 L11: 0.6540 L22: 0.9155 REMARK 3 L33: 1.9821 L12: 0.0347 REMARK 3 L13: -0.8775 L23: 0.4652 REMARK 3 S TENSOR REMARK 3 S11: 0.4459 S12: 0.1897 S13: 0.1951 REMARK 3 S21: 0.0831 S22: -0.1245 S23: 0.2604 REMARK 3 S31: 0.0723 S32: 0.2476 S33: 0.0856 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 33 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1433 -15.2784 -8.4444 REMARK 3 T TENSOR REMARK 3 T11: 0.5800 T22: 0.6384 REMARK 3 T33: 0.6700 T12: 0.0138 REMARK 3 T13: 0.2284 T23: -0.2653 REMARK 3 L TENSOR REMARK 3 L11: 2.8402 L22: 7.9757 REMARK 3 L33: 4.3429 L12: -1.8074 REMARK 3 L13: 0.5944 L23: 1.9463 REMARK 3 S TENSOR REMARK 3 S11: -0.2346 S12: -0.0341 S13: 0.7461 REMARK 3 S21: 0.1292 S22: 0.3688 S23: -0.3185 REMARK 3 S31: -0.2950 S32: -0.0904 S33: -0.1288 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 15 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.9543 -47.7013 -14.6124 REMARK 3 T TENSOR REMARK 3 T11: 0.6812 T22: 0.5187 REMARK 3 T33: 1.1045 T12: -0.0556 REMARK 3 T13: 0.2222 T23: -0.3412 REMARK 3 L TENSOR REMARK 3 L11: 4.5297 L22: 1.1867 REMARK 3 L33: 6.0112 L12: -0.3207 REMARK 3 L13: -1.6472 L23: 0.5624 REMARK 3 S TENSOR REMARK 3 S11: -0.0776 S12: 0.1997 S13: -1.0140 REMARK 3 S21: -0.6052 S22: 0.0422 S23: 0.0921 REMARK 3 S31: 0.5714 S32: 0.0496 S33: 0.1034 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 90 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4388 -48.6059 -6.3679 REMARK 3 T TENSOR REMARK 3 T11: 0.5732 T22: 0.5021 REMARK 3 T33: 1.0052 T12: -0.0479 REMARK 3 T13: 0.3083 T23: -0.1687 REMARK 3 L TENSOR REMARK 3 L11: 1.1314 L22: 1.2196 REMARK 3 L33: 8.9419 L12: -0.5143 REMARK 3 L13: 2.5145 L23: -1.1082 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: -0.1464 S13: -0.7306 REMARK 3 S21: -0.4400 S22: 0.2146 S23: -0.4471 REMARK 3 S31: 0.8595 S32: 0.5331 S33: -0.2380 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 133 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3857 -38.3148 -5.3438 REMARK 3 T TENSOR REMARK 3 T11: 0.3677 T22: 0.5683 REMARK 3 T33: 0.7268 T12: -0.1333 REMARK 3 T13: 0.1390 T23: -0.1683 REMARK 3 L TENSOR REMARK 3 L11: 3.2456 L22: 1.9556 REMARK 3 L33: 2.6904 L12: -1.2530 REMARK 3 L13: -0.0834 L23: -1.5415 REMARK 3 S TENSOR REMARK 3 S11: -0.0831 S12: -0.1439 S13: -0.8007 REMARK 3 S21: -0.1544 S22: 0.1061 S23: 0.3232 REMARK 3 S31: 0.3211 S32: -0.6352 S33: -0.0276 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 209 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.4312 -31.2233 -7.3035 REMARK 3 T TENSOR REMARK 3 T11: 0.3775 T22: 0.6658 REMARK 3 T33: 0.6601 T12: -0.0227 REMARK 3 T13: 0.0828 T23: -0.1499 REMARK 3 L TENSOR REMARK 3 L11: 6.0385 L22: 4.6061 REMARK 3 L33: 2.4642 L12: 0.7258 REMARK 3 L13: -1.2097 L23: -3.2419 REMARK 3 S TENSOR REMARK 3 S11: -0.3547 S12: 0.2153 S13: -0.1793 REMARK 3 S21: -0.4635 S22: 0.3521 S23: 0.8642 REMARK 3 S31: 0.3930 S32: -0.6532 S33: 0.1503 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 21 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9077 -59.5553 -46.3548 REMARK 3 T TENSOR REMARK 3 T11: 1.4812 T22: 0.9662 REMARK 3 T33: 1.1787 T12: 0.5372 REMARK 3 T13: 0.3472 T23: -1.2300 REMARK 3 L TENSOR REMARK 3 L11: 1.0788 L22: 1.6556 REMARK 3 L33: 2.1422 L12: 1.1932 REMARK 3 L13: 0.0768 L23: 0.9710 REMARK 3 S TENSOR REMARK 3 S11: -0.1687 S12: -0.0643 S13: -0.2261 REMARK 3 S21: 0.4284 S22: 0.0286 S23: 0.1449 REMARK 3 S31: 0.6492 S32: -0.2956 S33: 0.4638 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'F' AND (RESID 12 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5783 -64.6683 -51.2476 REMARK 3 T TENSOR REMARK 3 T11: 1.7448 T22: 1.2795 REMARK 3 T33: 1.0759 T12: 0.4792 REMARK 3 T13: 0.3992 T23: -0.7591 REMARK 3 L TENSOR REMARK 3 L11: 1.2408 L22: 1.0448 REMARK 3 L33: 0.0372 L12: -0.9666 REMARK 3 L13: 0.1921 L23: -0.1463 REMARK 3 S TENSOR REMARK 3 S11: 0.0528 S12: 0.1066 S13: 0.0761 REMARK 3 S21: 0.0198 S22: 0.0942 S23: -0.2971 REMARK 3 S31: -0.0747 S32: 0.0544 S33: -0.0363 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 7UFX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUNE 30, 2021 REMARK 200 DATA SCALING SOFTWARE : XSCALE JUNE 30, 2021, SCALA REMARK 200 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16760 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.01900 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: PHASER 2.8.2 REMARK 200 STARTING MODEL: 7U6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 180 MM MGCL2, 20% PEG 400, AND 100 MM REMARK 280 TRIS HCL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 37.40450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.74650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.55900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.40450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.74650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.55900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.40450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.74650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.55900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.40450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.74650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.55900 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET C -11 REMARK 465 ARG C -10 REMARK 465 GLY C -9 REMARK 465 SER C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 THR C 4 REMARK 465 ALA C 5 REMARK 465 VAL C 6 REMARK 465 ILE C 7 REMARK 465 ASN C 8 REMARK 465 HIS C 9 REMARK 465 LYS C 10 REMARK 465 LYS C 11 REMARK 465 ARG C 12 REMARK 465 LYS C 13 REMARK 465 ASN C 14 REMARK 465 ASP C 50 REMARK 465 GLY C 51 REMARK 465 THR C 52 REMARK 465 LEU C 53 REMARK 465 GLN C 54 REMARK 465 GLU C 55 REMARK 465 ARG C 98 REMARK 465 PRO C 99 REMARK 465 GLU C 100 REMARK 465 GLU C 101 REMARK 465 ASP C 102 REMARK 465 ALA C 103 REMARK 465 GLY C 104 REMARK 465 ASP C 105 REMARK 465 GLU C 106 REMARK 465 LYS C 107 REMARK 465 GLY C 108 REMARK 465 GLY C 141 REMARK 465 LEU C 142 REMARK 465 GLN C 143 REMARK 465 ASN C 144 REMARK 465 THR C 246 REMARK 465 SER C 247 REMARK 465 MET C 248 REMARK 465 THR C 249 REMARK 465 THR C 250 REMARK 465 GLY C 251 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 DA A -1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA A -1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA A -1 C2 N3 C4 REMARK 470 DA B 21 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA B 21 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA B 21 C2 N3 C4 REMARK 470 SER C 15 OG REMARK 470 LYS C 117 CE NZ REMARK 470 ARG C 145 CG CD NE CZ NH1 NH2 REMARK 470 DA E 20 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA E 20 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 20 C2 N3 C4 REMARK 470 DA F 11 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA F 11 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA F 11 C2 N3 C4 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 25 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 38 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG E 25 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG E 25 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC E 27 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC F 19 O4' - C1' - N1 ANGL. DEV. = 2.6 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 ASN C 132 108.25 -51.13 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 C 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 102 O REMARK 620 2 GLU C 77 OE2 121.7 REMARK 620 3 ASP C 81 OD1 122.1 106.2 REMARK 620 4 ASP C 81 OD2 103.4 131.3 56.3 REMARK 620 5 HOH C 401 O 61.7 62.4 131.1 165.1 REMARK 620 6 HOH C 402 O 106.7 68.6 61.2 117.4 71.0 REMARK 620 7 HOH C 403 O 59.7 104.8 79.3 113.8 61.1 49.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 42 OP1 REMARK 620 2 HOH E 101 O 106.7 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7RVA RELATED DB: PDB REMARK 900 7RVA CONTAINS THE SAME PROTEIN COMPLEXED TO A SHORTER DNA DUPLEX. REMARK 900 RELATED ID: 7U6K RELATED DB: PDB REMARK 900 7U6K WAS USED FOR MOLECULAR REPLACEMENT FOR THIS MODEL AND CONTAINS REMARK 900 THE SAME PROTEIN COMPLEXED TO A DIFFERENT DNA DUPLEX. DBREF 7UFX A -1 20 PDB 7UFX 7UFX -1 20 DBREF 7UFX B 21 42 PDB 7UFX 7UFX 21 42 DBREF 7UFX C 1 251 UNP P03856 REPE1_ECOLI 1 251 DBREF 7UFX E 20 30 PDB 7UFX 7UFX 20 30 DBREF 7UFX F 11 21 PDB 7UFX 7UFX 11 21 SEQADV 7UFX MET C -11 UNP P03856 INITIATING METHIONINE SEQADV 7UFX ARG C -10 UNP P03856 EXPRESSION TAG SEQADV 7UFX GLY C -9 UNP P03856 EXPRESSION TAG SEQADV 7UFX SER C -8 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -7 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -6 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -5 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -4 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -3 UNP P03856 EXPRESSION TAG SEQADV 7UFX HIS C -2 UNP P03856 EXPRESSION TAG SEQADV 7UFX GLY C -1 UNP P03856 EXPRESSION TAG SEQADV 7UFX SER C 0 UNP P03856 EXPRESSION TAG SEQADV 7UFX PRO C 118 UNP P03856 ARG 118 ENGINEERED MUTATION SEQRES 1 A 22 DA DA DC DC DT DG DT DG DA DC DA DA DA SEQRES 2 A 22 DT DT DG DC DC DC DT DC DA SEQRES 1 B 22 DA DT DC DT DG DA DG DG DG DC DA DA DT SEQRES 2 B 22 DT DT DG DT DC DA DC DA DG SEQRES 1 C 263 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 C 263 ALA GLU THR ALA VAL ILE ASN HIS LYS LYS ARG LYS ASN SEQRES 3 C 263 SER PRO ARG ILE VAL GLN SER ASN ASP LEU THR GLU ALA SEQRES 4 C 263 ALA TYR SER LEU SER ARG ASP GLN LYS ARG MET LEU TYR SEQRES 5 C 263 LEU PHE VAL ASP GLN ILE ARG LYS SER ASP GLY THR LEU SEQRES 6 C 263 GLN GLU HIS ASP GLY ILE CYS GLU ILE HIS VAL ALA LYS SEQRES 7 C 263 TYR ALA GLU ILE PHE GLY LEU THR SER ALA GLU ALA SER SEQRES 8 C 263 LYS ASP ILE ARG GLN ALA LEU LYS SER PHE ALA GLY LYS SEQRES 9 C 263 GLU VAL VAL PHE TYR ARG PRO GLU GLU ASP ALA GLY ASP SEQRES 10 C 263 GLU LYS GLY TYR GLU SER PHE PRO TRP PHE ILE LYS PRO SEQRES 11 C 263 ALA HIS SER PRO SER ARG GLY LEU TYR SER VAL HIS ILE SEQRES 12 C 263 ASN PRO TYR LEU ILE PRO PHE PHE ILE GLY LEU GLN ASN SEQRES 13 C 263 ARG PHE THR GLN PHE ARG LEU SER GLU THR LYS GLU ILE SEQRES 14 C 263 THR ASN PRO TYR ALA MET ARG LEU TYR GLU SER LEU CYS SEQRES 15 C 263 GLN TYR ARG LYS PRO ASP GLY SER GLY ILE VAL SER LEU SEQRES 16 C 263 LYS ILE ASP TRP ILE ILE GLU ARG TYR GLN LEU PRO GLN SEQRES 17 C 263 SER TYR GLN ARG MET PRO ASP PHE ARG ARG ARG PHE LEU SEQRES 18 C 263 GLN VAL CYS VAL ASN GLU ILE ASN SER ARG THR PRO MET SEQRES 19 C 263 ARG LEU SER TYR ILE GLU LYS LYS LYS GLY ARG GLN THR SEQRES 20 C 263 THR HIS ILE VAL PHE SER PHE ARG ASP ILE THR SER MET SEQRES 21 C 263 THR THR GLY SEQRES 1 E 11 DA DG DA DC DG DG DC DC DC DG DG SEQRES 1 F 11 DA DG DT DC DC DG DG DG DC DC DG HET MG B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG C 301 1 HET MG C 302 1 HET MG C 303 1 HETNAM MG MAGNESIUM ION FORMUL 6 MG 6(MG 2+) FORMUL 12 HOH *12(H2 O) HELIX 1 AA1 ASN C 22 GLU C 26 1 5 HELIX 2 AA2 SER C 32 LYS C 48 1 17 HELIX 3 AA3 VAL C 64 PHE C 71 1 8 HELIX 4 AA4 THR C 74 PHE C 89 1 16 HELIX 5 AA5 ASN C 132 TYR C 134 5 3 HELIX 6 AA6 LEU C 135 ILE C 140 1 6 HELIX 7 AA7 SER C 152 THR C 154 5 3 HELIX 8 AA8 ASN C 159 GLN C 171 1 13 HELIX 9 AA9 ILE C 185 GLN C 193 1 9 HELIX 10 AB1 PRO C 195 GLN C 199 5 5 HELIX 11 AB2 ARG C 200 PHE C 208 1 9 HELIX 12 AB3 PHE C 208 THR C 220 1 13 SHEET 1 AA1 2 ARG C 17 SER C 21 0 SHEET 2 AA1 2 PHE C 146 ARG C 150 -1 O THR C 147 N GLN C 20 SHEET 1 AA2 2 ILE C 59 HIS C 63 0 SHEET 2 AA2 2 LEU C 126 HIS C 130 -1 O VAL C 129 N CYS C 60 SHEET 1 AA3 2 GLU C 93 PHE C 96 0 SHEET 2 AA3 2 GLU C 110 PRO C 113 -1 O GLU C 110 N PHE C 96 SHEET 1 AA4 3 GLY C 179 LYS C 184 0 SHEET 2 AA4 3 GLN C 234 ASP C 244 -1 O PHE C 240 N VAL C 181 SHEET 3 AA4 3 MET C 222 LYS C 231 -1 N LYS C 231 O GLN C 234 LINK O HOH A 102 MG MG C 302 1555 1555 1.98 LINK OP1 DG B 42 MG MG B 101 1555 1555 2.40 LINK OP2 DG B 42 MG MG B 102 1555 4555 2.38 LINK MG MG B 101 O HOH E 101 1555 8444 2.02 LINK OE2 GLU C 77 MG MG C 302 1555 1555 1.99 LINK OD1 ASP C 81 MG MG C 302 1555 1555 2.03 LINK OD2 ASP C 81 MG MG C 302 1555 1555 2.53 LINK MG MG C 302 O HOH C 401 1555 1555 2.45 LINK MG MG C 302 O HOH C 402 1555 1555 2.87 LINK MG MG C 302 O HOH C 403 1555 1555 2.44 CRYST1 74.809 129.493 137.118 90.00 90.00 90.00 I 2 2 2 8 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 0.013367 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007293 0.00000