HEADER DNA BINDING PROTEIN/DNA 20-JUL-23 8TIR TITLE ISORETICULAR, INTERPENETRATING CO-CRYSTAL OF REPLICATION INITIATOR TITLE 2 PROTEIN REPE54 AND SYMMETRICAL EXPANDED DUPLEX (31MER) CONTAINING THE TITLE 3 COGNATE REPE54 SEQUENCE AND AN ADDITIONAL G-C RICH SEQUENCE WITH 1 TITLE 4 STICKY BASES AND 5' TERMINAL PHOSPHATES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(A*CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP COMPND 4 *CP*TP*CP*AP*GP*AP*CP*GP*G)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(A*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP COMPND 10 *CP*AP*GP*GP*TP*CP*CP*GP*G)-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 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: K-12; SOURCE 13 GENE: REPE, E, REP, ECOK12F045; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_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.ORUN,E.T.SHIELDS,R.SHRESTHA,C.K.SLAUGHTER,C.D.SNOW REVDAT 2 22-MAY-24 8TIR 1 REMARK REVDAT 1 02-AUG-23 8TIR 0 JRNL AUTH A.R.ORUN,A.VAJAPAYAJULA,S.DMYTRIW,E.T.SHIELDS,C.K.SLAUGHTER, JRNL AUTH 2 R.SHRESTHA,C.D.SNOW JRNL TITL TUNING CHEMICAL DNA LIGATION WITHIN DNA CRYSTALS AND JRNL TITL 2 CO-CRYSTALS. JRNL REF TO BE PUBLISHED JRNL REFN 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. 3.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1226 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 38.7400 - 6.4700 0.99 1307 145 0.1922 0.1822 REMARK 3 2 6.4600 - 5.1300 1.00 1254 143 0.2056 0.2631 REMARK 3 3 5.1300 - 4.4800 1.00 1235 136 0.1911 0.2128 REMARK 3 4 4.4800 - 4.0700 1.00 1209 131 0.1941 0.2378 REMARK 3 5 4.0700 - 3.7800 1.00 1226 134 0.2223 0.2883 REMARK 3 6 3.7800 - 3.5600 1.00 1217 141 0.2338 0.2962 REMARK 3 7 3.5600 - 3.3800 0.99 1187 135 0.2448 0.2631 REMARK 3 8 3.3800 - 3.2300 0.98 1217 123 0.2224 0.2653 REMARK 3 9 3.2300 - 3.1100 0.99 1177 138 0.3936 0.4619 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) : 0.428 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.36 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 : 0.013 3272 REMARK 3 ANGLE : 1.395 4695 REMARK 3 CHIRALITY : 0.087 511 REMARK 3 PLANARITY : 0.010 384 REMARK 3 DIHEDRAL : 27.382 867 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.8948 -7.5562 1.8737 REMARK 3 T TENSOR REMARK 3 T11: 0.7241 T22: 0.7769 REMARK 3 T33: 0.7315 T12: 0.0948 REMARK 3 T13: 0.0550 T23: -0.2969 REMARK 3 L TENSOR REMARK 3 L11: 0.0768 L22: 0.0768 REMARK 3 L33: 0.0338 L12: 0.0944 REMARK 3 L13: -0.0087 L23: -0.0250 REMARK 3 S TENSOR REMARK 3 S11: -0.0475 S12: -0.1487 S13: 0.2443 REMARK 3 S21: 0.2391 S22: 0.1149 S23: 0.0478 REMARK 3 S31: -0.2832 S32: -0.1791 S33: -0.0008 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 17 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0149 -40.1212 -30.4319 REMARK 3 T TENSOR REMARK 3 T11: 1.0152 T22: 0.9452 REMARK 3 T33: 0.7761 T12: 0.0554 REMARK 3 T13: 0.4966 T23: -0.7905 REMARK 3 L TENSOR REMARK 3 L11: 0.0756 L22: 0.0062 REMARK 3 L33: 0.0318 L12: 0.0122 REMARK 3 L13: -0.0193 L23: 0.0015 REMARK 3 S TENSOR REMARK 3 S11: 0.0212 S12: 0.1938 S13: -0.1291 REMARK 3 S21: -0.2400 S22: -0.0938 S23: -0.1485 REMARK 3 S31: 0.2704 S32: 0.0322 S33: 0.0080 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0923 -42.1682 -34.3152 REMARK 3 T TENSOR REMARK 3 T11: 1.3406 T22: 1.0691 REMARK 3 T33: 1.0718 T12: 0.3216 REMARK 3 T13: 0.7269 T23: -0.8426 REMARK 3 L TENSOR REMARK 3 L11: 0.2993 L22: 0.2493 REMARK 3 L33: 0.1733 L12: 0.0356 REMARK 3 L13: -0.2257 L23: -0.0699 REMARK 3 S TENSOR REMARK 3 S11: 0.3216 S12: 0.3181 S13: -0.1428 REMARK 3 S21: -0.2239 S22: 0.0600 S23: -0.0803 REMARK 3 S31: 0.3182 S32: 0.1745 S33: 0.2891 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1104 -11.3942 -0.3288 REMARK 3 T TENSOR REMARK 3 T11: 0.7674 T22: 0.7073 REMARK 3 T33: 0.5851 T12: -0.0846 REMARK 3 T13: 0.1405 T23: -0.2367 REMARK 3 L TENSOR REMARK 3 L11: 0.0459 L22: 0.1658 REMARK 3 L33: 0.0588 L12: -0.0419 REMARK 3 L13: 0.0403 L23: -0.1316 REMARK 3 S TENSOR REMARK 3 S11: -0.2448 S12: -0.0023 S13: 0.2278 REMARK 3 S21: 0.4364 S22: 0.0611 S23: -0.0770 REMARK 3 S31: -0.3258 S32: -0.0459 S33: -0.0579 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 14 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8452 -47.3458 -14.6860 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: 0.1864 REMARK 3 T33: 0.7690 T12: 0.2759 REMARK 3 T13: 0.5867 T23: -0.7362 REMARK 3 L TENSOR REMARK 3 L11: 0.0132 L22: 0.0289 REMARK 3 L33: 0.0499 L12: -0.0107 REMARK 3 L13: 0.0044 L23: 0.0352 REMARK 3 S TENSOR REMARK 3 S11: 0.0292 S12: 0.1113 S13: -0.2390 REMARK 3 S21: -0.2718 S22: 0.2163 S23: -0.1385 REMARK 3 S31: -0.0872 S32: 0.1241 S33: 0.2065 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 90 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3778 -48.3623 -6.2986 REMARK 3 T TENSOR REMARK 3 T11: 0.5708 T22: 0.6346 REMARK 3 T33: 1.0316 T12: 0.0189 REMARK 3 T13: 0.3038 T23: -0.1561 REMARK 3 L TENSOR REMARK 3 L11: -0.0009 L22: 0.0170 REMARK 3 L33: 0.0062 L12: -0.0226 REMARK 3 L13: -0.0040 L23: -0.0100 REMARK 3 S TENSOR REMARK 3 S11: 0.0261 S12: -0.1149 S13: -0.2383 REMARK 3 S21: -0.1470 S22: 0.1048 S23: -0.1387 REMARK 3 S31: 0.0453 S32: 0.0210 S33: -0.0003 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 133 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2467 -38.1707 -5.2465 REMARK 3 T TENSOR REMARK 3 T11: -0.1914 T22: 0.4390 REMARK 3 T33: 0.5347 T12: -0.0640 REMARK 3 T13: 0.4397 T23: -0.3507 REMARK 3 L TENSOR REMARK 3 L11: 0.0315 L22: 0.0990 REMARK 3 L33: 0.0334 L12: -0.0230 REMARK 3 L13: -0.0186 L23: 0.0274 REMARK 3 S TENSOR REMARK 3 S11: -0.1971 S12: -0.1026 S13: -0.2324 REMARK 3 S21: -0.1603 S22: -0.0013 S23: 0.0992 REMARK 3 S31: 0.0558 S32: -0.2479 S33: -0.0221 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 209 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.0023 -31.0217 -7.7603 REMARK 3 T TENSOR REMARK 3 T11: 0.4843 T22: 0.5866 REMARK 3 T33: 0.5189 T12: -0.0703 REMARK 3 T13: 0.0785 T23: -0.2003 REMARK 3 L TENSOR REMARK 3 L11: 0.0104 L22: 0.0114 REMARK 3 L33: 0.0090 L12: -0.0055 REMARK 3 L13: -0.0054 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: 0.0192 S13: 0.0656 REMARK 3 S21: -0.1360 S22: 0.1303 S23: 0.0422 REMARK 3 S31: 0.0293 S32: -0.0956 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 8TIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000266229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-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 JAN 31, 2020 REMARK 200 DATA SCALING SOFTWARE : XSCALE JAN 31, 2020, SCALA REMARK 200 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12327 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.110 REMARK 200 RESOLUTION RANGE LOW (A) : 38.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 1.20800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.810 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 350 MM MGCL2, 30% 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 37.21700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.71250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.04200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.21700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.71250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.04200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.21700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.71250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.04200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.21700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.71250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.04200 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: 6410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 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 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 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 2 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA B 2 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA B 2 C2 N3 C4 REMARK 470 ASN C 14 CG OD1 ND2 REMARK 470 ARG C 17 CG CD NE CZ NH1 NH2 REMARK 470 HIS C 56 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 117 CE NZ REMARK 470 ASN C 144 CG OD1 ND2 REMARK 470 ARG C 145 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N4 DC A 2 O6 DG B 3 5455 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A 2 O3' DC A 2 C3' -0.039 REMARK 500 DC A 4 O3' DC A 4 C3' -0.051 REMARK 500 DC B 5 O3' DC B 5 C3' -0.046 REMARK 500 DG B 14 O3' DG B 14 C3' -0.036 REMARK 500 VAL C 94 CB VAL C 94 CG2 -0.142 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 2 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 21 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 26 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 32 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 21 O3' - P - OP1 ANGL. DEV. = 6.6 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 27 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 28 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 32 O4' - C1' - N9 ANGL. DEV. = 3.3 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 132 108.65 -50.28 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 101 O REMARK 620 2 GLU C 77 OE2 66.0 REMARK 620 3 ASP C 81 OD1 120.2 83.0 REMARK 620 4 HOH C 401 O 86.7 119.8 65.7 REMARK 620 5 HOH C 402 O 48.7 61.2 71.7 60.6 REMARK 620 N 1 2 3 4 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 HOH A 102 O REMARK 620 2 HOH A 103 O 89.5 REMARK 620 3 HOH A 105 O 84.4 61.1 REMARK 620 4 DG B 27 OP1 86.1 142.4 81.3 REMARK 620 5 HOH B 202 O 150.6 87.3 68.6 78.9 REMARK 620 6 HOH B 206 O 119.5 89.8 143.3 124.6 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 27 OP2 REMARK 620 2 HOH B 201 O 50.3 REMARK 620 3 HOH B 203 O 61.7 17.4 REMARK 620 4 HOH B 204 O 53.6 3.4 14.8 REMARK 620 5 HOH B 205 O 47.6 11.0 14.2 11.6 REMARK 620 6 HOH B 207 O 59.7 16.7 2.2 14.5 12.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7U6K RELATED DB: PDB REMARK 900 ALSO A DESIGNED INTERPENTRATING, ISORETICULAR CO-CRYSTAL OF REPE54 REMARK 900 INITIATOR PROTEIN AND 31MER DNA DBREF 8TIR A 1 32 PDB 8TIR 8TIR 1 32 DBREF 8TIR B 2 33 PDB 8TIR 8TIR 2 33 DBREF 8TIR C 1 251 UNP P03856 REPE1_ECOLI 1 251 SEQADV 8TIR MET C -11 UNP P03856 INITIATING METHIONINE SEQADV 8TIR ARG C -10 UNP P03856 EXPRESSION TAG SEQADV 8TIR GLY C -9 UNP P03856 EXPRESSION TAG SEQADV 8TIR SER C -8 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -7 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -6 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -5 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -4 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -3 UNP P03856 EXPRESSION TAG SEQADV 8TIR HIS C -2 UNP P03856 EXPRESSION TAG SEQADV 8TIR GLY C -1 UNP P03856 EXPRESSION TAG SEQADV 8TIR SER C 0 UNP P03856 EXPRESSION TAG SEQADV 8TIR PRO C 118 UNP P03856 ARG 118 ENGINEERED MUTATION SEQRES 1 A 32 DA DC DC DC DG DG DA DC DC DT DG DT DG SEQRES 2 A 32 DA DC DA DA DA DT DT DG DC DC DC DT DC SEQRES 3 A 32 DA DG DA DC DG DG SEQRES 1 B 32 DA DG DC DC DG DT DC DT DG DA DG DG DG SEQRES 2 B 32 DC DA DA DT DT DT DG DT DC DA DC DA DG SEQRES 3 B 32 DG DT DC DC DG 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 HET MG B 101 1 HET MG B 102 1 HET MG C 301 1 HET MG C 302 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG 4(MG 2+) FORMUL 8 HOH *14(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 SER C 88 1 15 HELIX 5 AA5 LEU C 135 ILE C 140 1 6 HELIX 6 AA6 SER C 152 THR C 154 5 3 HELIX 7 AA7 ASN C 159 GLN C 171 1 13 HELIX 8 AA8 ILE C 185 GLN C 193 1 9 HELIX 9 AA9 PRO C 195 GLN C 199 5 5 HELIX 10 AB1 ARG C 200 PHE C 208 1 9 HELIX 11 AB2 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 3 ILE C 59 HIS C 63 0 SHEET 2 AA2 3 LEU C 126 ILE C 131 -1 O TYR C 127 N ILE C 62 SHEET 3 AA2 3 PHE C 115 HIS C 120 -1 N HIS C 120 O SER C 128 SHEET 1 AA3 2 GLU C 93 PHE C 96 0 SHEET 2 AA3 2 GLU C 110 PRO C 113 -1 O PHE C 112 N VAL C 94 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 ILE C 227 O VAL C 239 LINK O HOH A 101 MG MG C 301 1555 1555 2.67 LINK O HOH A 102 MG MG B 101 4555 1555 2.73 LINK O HOH A 103 MG MG B 101 4555 1555 2.01 LINK O HOH A 105 MG MG B 101 4555 1555 2.97 LINK OP1 DG B 27 MG MG B 101 1555 1555 2.10 LINK OP2 DG B 27 MG MG B 102 1555 4555 2.10 LINK MG MG B 101 O HOH B 202 1555 1555 2.14 LINK MG MG B 101 O HOH B 206 1555 4555 2.29 LINK MG MG B 102 O HOH B 201 1555 4555 3.00 LINK MG MG B 102 O HOH B 203 1555 4555 2.07 LINK MG MG B 102 O HOH B 204 1555 4555 2.29 LINK MG MG B 102 O HOH B 205 1555 1555 2.41 LINK MG MG B 102 O HOH B 207 1555 1555 2.06 LINK OE2 GLU C 77 MG MG C 301 1555 1555 2.35 LINK OD1 ASP C 81 MG MG C 301 1555 1555 2.40 LINK MG MG C 301 O HOH C 401 1555 1555 2.54 LINK MG MG C 301 O HOH C 402 1555 1555 2.92 CRYST1 74.434 131.425 136.084 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 0.013435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007348 0.00000