HEADER DNA BINDING PROTEIN/DNA 07-JUN-22 8D86 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 CO- TITLE 4 CRYSTALLIZED WITH A GUEST SMALL MOLECULE, NETROPSIN. 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*GP*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*CP*CP*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: 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.ORUN,C.D.SNOW REVDAT 3 01-NOV-23 8D86 1 JRNL REVDAT 2 25-OCT-23 8D86 1 REMARK REVDAT 1 28-JUN-23 8D86 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. 3.12 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) : 3.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1201 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 38.3200 - 6.4800 0.99 1294 141 0.1742 0.1827 REMARK 3 2 6.4800 - 5.1500 1.00 1234 141 0.1934 0.2291 REMARK 3 3 5.1500 - 4.5000 1.00 1217 133 0.1645 0.1845 REMARK 3 4 4.5000 - 4.0900 1.00 1202 133 0.1722 0.2374 REMARK 3 5 4.0900 - 3.8000 1.00 1204 131 0.2001 0.2877 REMARK 3 6 3.7900 - 3.5700 1.00 1198 134 0.2083 0.2830 REMARK 3 7 3.5700 - 3.3900 0.99 1167 132 0.2118 0.2595 REMARK 3 8 3.3900 - 3.2500 0.97 1158 126 0.2143 0.2731 REMARK 3 9 3.2400 - 3.1200 0.99 1200 130 0.3613 0.4644 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) : 0.442 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.34 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 : 0.014 3322 REMARK 3 ANGLE : 1.572 4763 REMARK 3 CHIRALITY : 0.087 513 REMARK 3 PLANARITY : 0.012 394 REMARK 3 DIHEDRAL : 27.241 880 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 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.3053 -8.4913 0.8098 REMARK 3 T TENSOR REMARK 3 T11: 0.7510 T22: 0.8607 REMARK 3 T33: 0.8757 T12: 0.0855 REMARK 3 T13: 0.0975 T23: -0.2940 REMARK 3 L TENSOR REMARK 3 L11: 0.7508 L22: 2.1000 REMARK 3 L33: 2.3883 L12: 0.1779 REMARK 3 L13: -0.2148 L23: 0.8795 REMARK 3 S TENSOR REMARK 3 S11: 0.0875 S12: -0.2050 S13: 0.7194 REMARK 3 S21: 0.0332 S22: 0.1236 S23: -0.5559 REMARK 3 S31: -0.3905 S32: -0.4621 S33: -0.1341 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3479 -41.8669 -31.9068 REMARK 3 T TENSOR REMARK 3 T11: 1.6999 T22: 1.3726 REMARK 3 T33: 1.1531 T12: 0.1325 REMARK 3 T13: 0.5561 T23: -0.5814 REMARK 3 L TENSOR REMARK 3 L11: 0.6804 L22: 1.1491 REMARK 3 L33: 0.6187 L12: -0.6170 REMARK 3 L13: -0.4453 L23: 0.7958 REMARK 3 S TENSOR REMARK 3 S11: 0.1220 S12: 0.6544 S13: -0.2958 REMARK 3 S21: -0.5737 S22: -0.0106 S23: -0.6725 REMARK 3 S31: 0.9429 S32: 0.2420 S33: -0.0313 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6156 -44.1791 -35.1338 REMARK 3 T TENSOR REMARK 3 T11: 1.8465 T22: 1.5565 REMARK 3 T33: 1.4210 T12: 0.4113 REMARK 3 T13: 0.8408 T23: -0.9575 REMARK 3 L TENSOR REMARK 3 L11: 0.4087 L22: 0.8877 REMARK 3 L33: 0.4738 L12: 0.2525 REMARK 3 L13: -0.2126 L23: 0.4837 REMARK 3 S TENSOR REMARK 3 S11: 1.0237 S12: 0.5864 S13: -0.0528 REMARK 3 S21: -0.3168 S22: -0.3125 S23: -0.3651 REMARK 3 S31: 0.4036 S32: 0.1824 S33: 0.2930 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2088 -12.1517 -1.8364 REMARK 3 T TENSOR REMARK 3 T11: 0.8712 T22: 0.7501 REMARK 3 T33: 0.5843 T12: -0.0162 REMARK 3 T13: 0.2118 T23: -0.1209 REMARK 3 L TENSOR REMARK 3 L11: 1.0276 L22: 1.8417 REMARK 3 L33: 0.9564 L12: -0.1615 REMARK 3 L13: 0.9833 L23: -0.4643 REMARK 3 S TENSOR REMARK 3 S11: -0.4077 S12: -0.1947 S13: 0.1617 REMARK 3 S21: 0.4995 S22: 0.2071 S23: -0.3449 REMARK 3 S31: -0.1209 S32: 0.0878 S33: 0.3623 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 15 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8287 -47.6290 -14.6933 REMARK 3 T TENSOR REMARK 3 T11: 0.6695 T22: 0.6376 REMARK 3 T33: 1.0997 T12: -0.0027 REMARK 3 T13: 0.2461 T23: -0.3413 REMARK 3 L TENSOR REMARK 3 L11: 1.1378 L22: 0.9442 REMARK 3 L33: 1.2955 L12: -0.0960 REMARK 3 L13: -0.0039 L23: 0.0495 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.4026 S13: -0.7015 REMARK 3 S21: -0.5348 S22: 0.2350 S23: 0.0189 REMARK 3 S31: -0.0519 S32: 0.0341 S33: -0.0671 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 90 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4141 -48.7214 -6.3788 REMARK 3 T TENSOR REMARK 3 T11: 0.6413 T22: 0.7104 REMARK 3 T33: 1.3955 T12: -0.0114 REMARK 3 T13: 0.4099 T23: -0.1867 REMARK 3 L TENSOR REMARK 3 L11: 1.3337 L22: 0.8231 REMARK 3 L33: 1.5490 L12: 0.0973 REMARK 3 L13: 0.1821 L23: -0.9216 REMARK 3 S TENSOR REMARK 3 S11: -0.2471 S12: -0.3346 S13: -0.9218 REMARK 3 S21: -0.1618 S22: 0.2679 S23: -0.4866 REMARK 3 S31: 0.3386 S32: 0.5233 S33: -0.0113 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 133 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.1600 -38.2379 -5.2871 REMARK 3 T TENSOR REMARK 3 T11: 0.4830 T22: 0.6126 REMARK 3 T33: 0.9312 T12: -0.0730 REMARK 3 T13: 0.2347 T23: -0.1720 REMARK 3 L TENSOR REMARK 3 L11: 0.7046 L22: 1.0793 REMARK 3 L33: 1.2546 L12: -0.2787 REMARK 3 L13: 0.0020 L23: -0.3531 REMARK 3 S TENSOR REMARK 3 S11: -0.2505 S12: -0.1099 S13: -0.9815 REMARK 3 S21: 0.0616 S22: 0.0032 S23: 0.2614 REMARK 3 S31: 0.1323 S32: -0.1455 S33: 0.1974 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 209 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.9056 -30.8730 -7.7938 REMARK 3 T TENSOR REMARK 3 T11: 0.5464 T22: 0.6080 REMARK 3 T33: 0.7958 T12: -0.0559 REMARK 3 T13: 0.1196 T23: -0.1174 REMARK 3 L TENSOR REMARK 3 L11: 2.2925 L22: 3.1839 REMARK 3 L33: 3.5787 L12: 0.3232 REMARK 3 L13: -0.0954 L23: 1.2515 REMARK 3 S TENSOR REMARK 3 S11: -0.0747 S12: 0.3544 S13: -0.0150 REMARK 3 S21: -0.3972 S22: 0.4323 S23: 0.1673 REMARK 3 S31: -0.2829 S32: -0.4304 S33: -0.1672 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 8D86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000264885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-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 : 12130 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.120 REMARK 200 RESOLUTION RANGE LOW (A) : 38.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 1.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.840 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 (%): 66.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MM MGCL2, 25% 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 37.07500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.36550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 67.13050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.07500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.36550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.13050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.07500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.36550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.13050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.07500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.36550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.13050 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: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 LEU C 142 REMARK 465 GLN C 143 REMARK 465 ASN C 144 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 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA B 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA B 1 C2 N3 C4 REMARK 470 ARG C 17 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 57 CG OD1 OD2 REMARK 470 LYS C 117 CE NZ REMARK 470 ARG C 145 CG CD NE CZ NH1 NH2 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 OP2 DG B 27 O HOH B 201 2.08 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 3 C1' DC A 3 N1 0.087 REMARK 500 DA A 18 N9 DA A 18 C4 0.047 REMARK 500 DC A 26 O3' DC A 26 C3' -0.043 REMARK 500 DC B 8 C1' DC B 8 N1 0.092 REMARK 500 DG B 13 O3' DG B 13 C3' -0.060 REMARK 500 DT B 20 C1' DT B 20 N1 0.092 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' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA A 17 O5' - P - OP2 ANGL. DEV. = -8.9 DEGREES REMARK 500 DG A 21 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC A 26 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 32 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 24 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 27 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 DG B 27 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 28 O3' - P - OP2 ANGL. DEV. = 9.3 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 ASP C 57 -88.01 -95.31 REMARK 500 ASN C 132 108.98 -50.33 REMARK 500 THR C 246 58.98 -97.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 208 O 102.1 REMARK 620 3 HOH B 204 O 72.1 167.3 REMARK 620 N 1 2 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 201 O REMARK 620 2 GLU C 77 OE2 80.2 REMARK 620 3 ASP C 81 OD1 116.6 79.8 REMARK 620 4 HOH C 402 O 106.2 63.3 116.5 REMARK 620 5 HOH C 403 O 121.5 151.0 73.3 120.2 REMARK 620 6 HOH C 404 O 164.4 84.7 63.9 62.9 74.0 REMARK 620 N 1 2 3 4 5 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 202 O REMARK 620 2 HOH A 204 O 78.7 REMARK 620 3 HOH A 205 O 71.5 83.3 REMARK 620 4 DG B 27 OP1 151.6 82.5 85.3 REMARK 620 5 HOH B 203 O 107.6 156.4 77.5 82.3 REMARK 620 6 HOH B 205 O 84.8 117.2 145.3 123.0 86.3 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 72.3 REMARK 620 3 HOH B 202 O 74.7 3.1 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7U6K RELATED DB: PDB REMARK 900 7U6K CONTAINS THE SAME PROTEIN COMPLEXED TO THE SAME DNA DUPLEX BUT REMARK 900 NO NETROPSIN. 7U6K WAS THE STARTING MODEL FOR THIS STRUCTURE. DBREF 8D86 A 1 32 PDB 8D86 8D86 1 32 DBREF 8D86 B 1 32 PDB 8D86 8D86 1 32 DBREF 8D86 C 1 251 UNP P03856 REPE1_ECOLI 1 251 SEQADV 8D86 MET C -11 UNP P03856 INITIATING METHIONINE SEQADV 8D86 ARG C -10 UNP P03856 EXPRESSION TAG SEQADV 8D86 GLY C -9 UNP P03856 EXPRESSION TAG SEQADV 8D86 SER C -8 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -7 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -6 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -5 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -4 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -3 UNP P03856 EXPRESSION TAG SEQADV 8D86 HIS C -2 UNP P03856 EXPRESSION TAG SEQADV 8D86 GLY C -1 UNP P03856 EXPRESSION TAG SEQADV 8D86 SER C 0 UNP P03856 EXPRESSION TAG SEQADV 8D86 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 DG 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 DC DC 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 A 101 1 HET MG A 102 1 HET MG B 101 1 HET MG B 102 1 HET NT B 103 31 HET MG C 301 1 HETNAM MG MAGNESIUM ION HETNAM NT NETROPSIN FORMUL 4 MG 5(MG 2+) FORMUL 8 NT C18 H26 N10 O3 FORMUL 10 HOH *17(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 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 TYR C 192 1 8 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 ILE C 227 O VAL C 239 LINK MG MG A 101 O HOH A 203 1555 1555 2.42 LINK MG MG A 101 O HOH A 208 1555 1555 2.55 LINK MG MG A 101 O HOH B 204 1555 4555 2.06 LINK O HOH A 201 MG MG C 301 1555 1555 2.02 LINK O HOH A 202 MG MG B 101 4555 1555 1.86 LINK O HOH A 204 MG MG B 101 4555 1555 2.97 LINK O HOH A 205 MG MG B 101 4555 1555 2.78 LINK OP1 DG B 27 MG MG B 101 1555 1555 2.04 LINK OP2 DG B 27 MG MG B 102 1555 4555 2.79 LINK MG MG B 101 O HOH B 203 1555 1555 2.28 LINK MG MG B 101 O HOH B 205 1555 4555 2.36 LINK MG MG B 102 O HOH B 201 1555 4555 2.21 LINK MG MG B 102 O HOH B 202 1555 4555 1.83 LINK OE2 GLU C 77 MG MG C 301 1555 1555 2.27 LINK OD1 ASP C 81 MG MG C 301 1555 1555 2.69 LINK MG MG C 301 O HOH C 402 1555 1555 2.30 LINK MG MG C 301 O HOH C 403 1555 1555 1.83 LINK MG MG C 301 O HOH C 404 1555 1555 2.62 CRYST1 74.150 132.731 134.261 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 0.013486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007448 0.00000