HEADER DNA BINDING PROTEIN/DNA 07-MAR-22 7U7O 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 T-A RICH SEQUENCE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(A*TP*AP*AP*TP*TP*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*TP*AP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP COMPND 10 *AP*CP*AP*GP*GP*TP*AP*AP*T)-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: K12; 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 EXPDTA X-RAY DIFFRACTION AUTHOR A.R.WARD,C.D.SNOW REVDAT 3 01-NOV-23 7U7O 1 JRNL REVDAT 2 25-OCT-23 7U7O 1 REMARK REVDAT 1 29-MAR-23 7U7O 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. 2.97 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) : 2.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 12639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 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 37.4200 - 6.1700 1.00 1379 154 0.1940 0.1861 REMARK 3 2 6.1700 - 4.9000 1.00 1329 149 0.2000 0.2254 REMARK 3 3 4.9000 - 4.2800 1.00 1297 143 0.1994 0.1972 REMARK 3 4 4.2800 - 3.8900 0.95 1241 135 0.2191 0.2527 REMARK 3 5 3.8900 - 3.6100 0.91 1166 133 0.3658 0.3986 REMARK 3 6 3.6100 - 3.4000 0.93 1180 133 0.3450 0.3688 REMARK 3 7 3.4000 - 3.2300 0.96 1241 137 0.2434 0.2518 REMARK 3 8 3.2300 - 3.0900 0.98 1246 135 0.2405 0.2724 REMARK 3 9 3.0900 - 2.9700 1.00 1296 145 0.4429 0.4531 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.302 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.57 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 3323 REMARK 3 ANGLE : 0.897 4761 REMARK 3 CHIRALITY : 0.057 516 REMARK 3 PLANARITY : 0.007 393 REMARK 3 DIHEDRAL : 28.896 874 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -6 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8298 -10.2743 1.7964 REMARK 3 T TENSOR REMARK 3 T11: 1.1878 T22: 0.8816 REMARK 3 T33: 0.9822 T12: 0.1983 REMARK 3 T13: 0.2944 T23: -0.5129 REMARK 3 L TENSOR REMARK 3 L11: 2.5037 L22: 1.8043 REMARK 3 L33: 0.0154 L12: -1.0219 REMARK 3 L13: 0.0930 L23: -0.1768 REMARK 3 S TENSOR REMARK 3 S11: 0.1176 S12: -0.4478 S13: 1.0221 REMARK 3 S21: 0.6755 S22: 0.0349 S23: -0.3886 REMARK 3 S31: -0.8662 S32: -0.1041 S33: -0.4876 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9102 -42.3709 -30.4639 REMARK 3 T TENSOR REMARK 3 T11: 1.3736 T22: 1.0785 REMARK 3 T33: 0.6434 T12: 0.2407 REMARK 3 T13: 0.3343 T23: -0.5609 REMARK 3 L TENSOR REMARK 3 L11: 0.8303 L22: 0.5040 REMARK 3 L33: 0.4941 L12: -0.4420 REMARK 3 L13: -0.6342 L23: 0.2745 REMARK 3 S TENSOR REMARK 3 S11: 0.0866 S12: 0.7646 S13: -0.3702 REMARK 3 S21: -0.6717 S22: -0.0435 S23: -0.3798 REMARK 3 S31: 0.6889 S32: 0.2550 S33: 0.0716 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 16 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2853 -59.0490 -43.8935 REMARK 3 T TENSOR REMARK 3 T11: 2.0390 T22: 1.4580 REMARK 3 T33: 1.5030 T12: 0.4280 REMARK 3 T13: 0.4068 T23: -0.7657 REMARK 3 L TENSOR REMARK 3 L11: 0.6443 L22: 2.6364 REMARK 3 L33: 0.0297 L12: -0.6235 REMARK 3 L13: -0.1234 L23: 0.2245 REMARK 3 S TENSOR REMARK 3 S11: -0.0287 S12: 0.1559 S13: -0.1840 REMARK 3 S21: -0.2018 S22: 0.0170 S23: -0.3918 REMARK 3 S31: 0.2344 S32: 0.1541 S33: 0.0019 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 22 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0353 -47.9349 -33.7775 REMARK 3 T TENSOR REMARK 3 T11: 1.3446 T22: 1.0239 REMARK 3 T33: 0.7872 T12: 0.2221 REMARK 3 T13: 0.2618 T23: -0.4413 REMARK 3 L TENSOR REMARK 3 L11: 7.0131 L22: 5.9378 REMARK 3 L33: 6.6465 L12: 1.0239 REMARK 3 L13: 2.9936 L23: 4.3599 REMARK 3 S TENSOR REMARK 3 S11: -0.1570 S12: 0.7057 S13: -0.1912 REMARK 3 S21: -0.9811 S22: -0.0592 S23: 0.0858 REMARK 3 S31: -0.2722 S32: 0.0077 S33: 0.0772 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7400 -31.8882 -25.4925 REMARK 3 T TENSOR REMARK 3 T11: 1.1904 T22: 0.8454 REMARK 3 T33: 0.9512 T12: -0.0542 REMARK 3 T13: 0.5192 T23: -0.3030 REMARK 3 L TENSOR REMARK 3 L11: 6.4864 L22: 9.7819 REMARK 3 L33: 1.3464 L12: -6.5486 REMARK 3 L13: -2.6996 L23: 3.4372 REMARK 3 S TENSOR REMARK 3 S11: 0.2425 S12: 0.1913 S13: 0.6187 REMARK 3 S21: -0.0540 S22: 0.2465 S23: -0.6785 REMARK 3 S31: -0.5352 S32: 0.1199 S33: -0.5123 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 14 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6222 -48.6283 -14.3360 REMARK 3 T TENSOR REMARK 3 T11: 0.5619 T22: 0.4345 REMARK 3 T33: 0.4630 T12: -0.0346 REMARK 3 T13: 0.0932 T23: -0.2677 REMARK 3 L TENSOR REMARK 3 L11: 2.1809 L22: 0.8435 REMARK 3 L33: 3.9460 L12: -0.7444 REMARK 3 L13: -0.4389 L23: -1.3349 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.3481 S13: -0.9168 REMARK 3 S21: -0.8392 S22: -0.0231 S23: 0.1819 REMARK 3 S31: 0.7025 S32: -0.1323 S33: 0.0780 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 90 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4514 -49.8075 -5.8714 REMARK 3 T TENSOR REMARK 3 T11: 0.4220 T22: 0.4333 REMARK 3 T33: 0.4669 T12: 0.2088 REMARK 3 T13: 0.0077 T23: -0.0894 REMARK 3 L TENSOR REMARK 3 L11: 1.9616 L22: 2.5654 REMARK 3 L33: 6.5206 L12: 1.6447 REMARK 3 L13: -0.1705 L23: -1.8378 REMARK 3 S TENSOR REMARK 3 S11: 0.2911 S12: 0.1184 S13: -0.4150 REMARK 3 S21: 0.0069 S22: 0.2495 S23: -0.2537 REMARK 3 S31: 0.2749 S32: -0.0490 S33: -0.5309 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 133 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6390 -39.8071 -4.9399 REMARK 3 T TENSOR REMARK 3 T11: 0.2830 T22: 0.4787 REMARK 3 T33: 0.3541 T12: -0.0737 REMARK 3 T13: 0.0519 T23: -0.1157 REMARK 3 L TENSOR REMARK 3 L11: 3.3919 L22: 2.7733 REMARK 3 L33: 2.8480 L12: -1.0120 REMARK 3 L13: -0.0225 L23: -1.4797 REMARK 3 S TENSOR REMARK 3 S11: 0.0934 S12: -0.0521 S13: -0.5303 REMARK 3 S21: -0.1309 S22: -0.0688 S23: 0.4788 REMARK 3 S31: 0.3104 S32: -0.6157 S33: -0.0354 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 32 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2835 -24.6253 -16.9198 REMARK 3 T TENSOR REMARK 3 T11: 0.8159 T22: 0.4735 REMARK 3 T33: 0.4622 T12: -0.0232 REMARK 3 T13: 0.3630 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 4.1592 L22: 1.0450 REMARK 3 L33: 4.5004 L12: 0.0286 REMARK 3 L13: -1.4319 L23: 0.3789 REMARK 3 S TENSOR REMARK 3 S11: 0.1886 S12: 0.3718 S13: 0.3828 REMARK 3 S21: -0.9292 S22: -0.3724 S23: -0.1580 REMARK 3 S31: -0.0311 S32: 0.0436 S33: 0.1361 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 37 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.0013 -10.2639 3.8423 REMARK 3 T TENSOR REMARK 3 T11: 1.2930 T22: 0.8881 REMARK 3 T33: 1.1190 T12: 0.1788 REMARK 3 T13: 0.3430 T23: -0.5843 REMARK 3 L TENSOR REMARK 3 L11: 2.7140 L22: 0.3476 REMARK 3 L33: 0.5523 L12: -0.9711 REMARK 3 L13: -1.2262 L23: 0.4439 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: -0.4531 S13: 0.4054 REMARK 3 S21: 0.8130 S22: 0.0257 S23: 0.4638 REMARK 3 S31: -0.7118 S32: -0.5268 S33: 0.2900 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 209 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4592 -32.8476 -8.0084 REMARK 3 T TENSOR REMARK 3 T11: 0.2027 T22: 0.6750 REMARK 3 T33: 0.4460 T12: 0.0583 REMARK 3 T13: -0.0113 T23: -0.1534 REMARK 3 L TENSOR REMARK 3 L11: 1.6586 L22: 5.3438 REMARK 3 L33: 6.9312 L12: -1.5613 REMARK 3 L13: -2.9538 L23: 0.2420 REMARK 3 S TENSOR REMARK 3 S11: -0.0376 S12: -0.2617 S13: 0.4300 REMARK 3 S21: -0.2305 S22: 0.0596 S23: 0.7579 REMARK 3 S31: 0.2957 S32: -0.5388 S33: 0.0177 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 7U7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-20 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 : 13010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.970 REMARK 200 RESOLUTION RANGE LOW (A) : 37.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.93500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 63.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MM MGCL2, 28% PEG 400, AND 80 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 36.07050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.56200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.64500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.07050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.56200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.64500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.07050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.56200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.64500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.07050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.56200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.64500 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: 6030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 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 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 -6 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA A -6 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA A -6 C2 N3 C4 REMARK 470 DA B 16 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA B 16 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA B 16 C2 N3 C4 REMARK 470 ARG C 98 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 144 CG OD1 ND2 REMARK 470 MET C 248 CG SD CE 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 O ILE C 216 OG1 THR C 220 2.07 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 25 O4' - C1' - N9 ANGL. DEV. = 2.7 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 132 107.94 -50.21 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 103 O REMARK 620 2 HOH A 104 O 77.6 REMARK 620 3 GLU C 77 OE2 104.8 133.3 REMARK 620 4 ASP C 81 OD1 100.8 141.0 85.2 REMARK 620 5 HOH C 404 O 137.6 76.8 71.1 120.3 REMARK 620 6 HOH C 405 O 93.5 65.4 155.9 76.0 105.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES 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. REMARK 900 RELATED ID: 7RVA RELATED DB: PDB REMARK 900 7RVA CONTAINS THE SAME PROTEIN COMPLEXED TO A SHORTER DNA DUPLEX. DBREF 7U7O A -6 25 PDB 7U7O 7U7O -6 25 DBREF 7U7O B 16 47 PDB 7U7O 7U7O 16 47 DBREF 7U7O C 1 251 UNP P03856 REPE1_ECOLI 1 251 SEQADV 7U7O MET C -11 UNP P03856 INITIATING METHIONINE SEQADV 7U7O ARG C -10 UNP P03856 EXPRESSION TAG SEQADV 7U7O GLY C -9 UNP P03856 EXPRESSION TAG SEQADV 7U7O SER C -8 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -7 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -6 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -5 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -4 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -3 UNP P03856 EXPRESSION TAG SEQADV 7U7O HIS C -2 UNP P03856 EXPRESSION TAG SEQADV 7U7O GLY C -1 UNP P03856 EXPRESSION TAG SEQADV 7U7O SER C 0 UNP P03856 EXPRESSION TAG SEQADV 7U7O PRO C 118 UNP P03856 ARG 118 ENGINEERED MUTATION SEQRES 1 A 32 DA DT DA DA DT DT 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 DT DA DC DC DG DT DC DT DG DA DG DG SEQRES 2 B 32 DG DC DA DA DT DT DT DG DT DC DA DC DA SEQRES 3 B 32 DG DG DT DA DA DT 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 C 301 1 HETNAM MG MAGNESIUM ION FORMUL 4 MG MG 2+ FORMUL 5 HOH *26(H2 O) HELIX 1 AA1 ASN C 22 GLU C 26 1 5 HELIX 2 AA2 SER C 32 SER C 49 1 18 HELIX 3 AA3 VAL C 64 GLY C 72 1 9 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 LEU C 151 LYS C 155 1 5 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 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 ARG C 223 O ARG C 243 LINK O HOH A 103 MG MG C 301 1555 1555 2.14 LINK O HOH A 104 MG MG C 301 1555 1555 1.92 LINK OE2 GLU C 77 MG MG C 301 1555 1555 2.30 LINK OD1 ASP C 81 MG MG C 301 1555 1555 2.05 LINK MG MG C 301 O HOH C 404 1555 1555 2.16 LINK MG MG C 301 O HOH C 405 1555 1555 2.30 CRYST1 72.141 129.124 131.290 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 0.013862 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007617 0.00000