HEADER HYDROLASE/DNA 29-MAY-13 4KYW TITLE RESTRICTION ENDONUCLEASE DPNI IN COMPLEX WITH TWO DNA MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-2 RESTRICTION ENZYME DPNI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: R.DPNI, ENDONUCLEASE DPNI, TYPE II RESTRICTION ENZYME DPNI; COMPND 5 EC: 3.1.21.4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3'; COMPND 9 CHAIN: C, D, E, F; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 170187; SOURCE 4 STRAIN: TIGR4; SOURCE 5 GENE: DPNC, SPR1665, SP_1850; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2925; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS RESTRICTION ENDONUCLEASE-DNA COMPLEX, TYPE IIM, TYPE IIE, RESTRICTION KEYWDS 2 ENZYME, DPNI, METHYLATION DEPENDENT, N6-METHYLADENINE, PD-(D/E)XK KEYWDS 3 TYPE ENDONUCLEASE, WINGED HELIX DOMAIN, RESTRICTION ENDONUCLEASE, KEYWDS 4 DNA BINDING, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.MIERZEJEWSKA,W.SIWEK,H.CZAPINSKA,K.SKOWRONEK,J.M.BUJNICKI, AUTHOR 2 M.BOCHTLER REVDAT 6 20-SEP-23 4KYW 1 REMARK SEQADV LINK REVDAT 5 07-MAR-18 4KYW 1 REMARK REVDAT 4 20-AUG-14 4KYW 1 JRNL REVDAT 3 09-JUL-14 4KYW 1 JRNL REVDAT 2 02-JUL-14 4KYW 1 JRNL REVDAT 1 04-JUN-14 4KYW 0 JRNL AUTH K.MIERZEJEWSKA,W.SIWEK,H.CZAPINSKA,M.KAUS-DROBEK, JRNL AUTH 2 M.RADLINSKA,K.SKOWRONEK,J.M.BUJNICKI,M.DADLEZ,M.BOCHTLER JRNL TITL STRUCTURAL BASIS OF THE METHYLATION SPECIFICITY OF R.DPNI. JRNL REF NUCLEIC ACIDS RES. V. 42 8745 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24966351 JRNL DOI 10.1093/NAR/GKU546 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 23477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1204 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2096 REMARK 3 NUCLEIC ACID ATOMS : 812 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : 1.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.263 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3070 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1910 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4302 ; 1.340 ; 2.288 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4674 ; 3.804 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 6.217 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;37.887 ;24.435 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;15.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.589 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2828 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 540 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 539 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2004 ; 0.273 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1368 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1332 ; 0.109 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 135 ; 0.189 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.071 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.218 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 18 ; 0.222 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.212 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1279 ; 0.675 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 513 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2076 ; 1.282 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1791 ; 1.794 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2226 ; 2.848 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 182 REMARK 3 RESIDUE RANGE : A 301 A 302 REMARK 3 RESIDUE RANGE : A 303 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): -35.8980 61.7160 -44.5240 REMARK 3 T TENSOR REMARK 3 T11: 0.0605 T22: 0.1110 REMARK 3 T33: -0.0444 T12: -0.0136 REMARK 3 T13: 0.0163 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.9863 L22: 1.6433 REMARK 3 L33: 2.5057 L12: -0.6052 REMARK 3 L13: 0.2395 L23: -0.0195 REMARK 3 S TENSOR REMARK 3 S11: -0.0248 S12: 0.0654 S13: 0.1812 REMARK 3 S21: -0.1073 S22: 0.0293 S23: -0.1441 REMARK 3 S31: 0.1609 S32: 0.3614 S33: -0.0045 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 183 A 254 REMARK 3 ORIGIN FOR THE GROUP (A): -12.9170 49.8850 -23.0390 REMARK 3 T TENSOR REMARK 3 T11: -0.0626 T22: 0.0333 REMARK 3 T33: 0.1340 T12: 0.1251 REMARK 3 T13: 0.0749 T23: 0.0426 REMARK 3 L TENSOR REMARK 3 L11: 5.2790 L22: 3.2687 REMARK 3 L33: 6.9367 L12: -0.4907 REMARK 3 L13: -1.1320 L23: -0.5751 REMARK 3 S TENSOR REMARK 3 S11: -0.1319 S12: 0.0292 S13: 0.2313 REMARK 3 S21: 0.0068 S22: 0.1811 S23: -0.2340 REMARK 3 S31: -0.2114 S32: 0.0806 S33: -0.0492 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 10 REMARK 3 RESIDUE RANGE : D 1 D 10 REMARK 3 ORIGIN FOR THE GROUP (A): -50.8430 68.4980 -47.6200 REMARK 3 T TENSOR REMARK 3 T11: 0.0762 T22: 0.1011 REMARK 3 T33: 0.0684 T12: -0.0555 REMARK 3 T13: -0.0744 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.9907 L22: 1.3154 REMARK 3 L33: 2.7803 L12: -1.0393 REMARK 3 L13: -0.9890 L23: 0.5438 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: -0.0771 S13: 0.1352 REMARK 3 S21: -0.3531 S22: -0.1622 S23: 0.2124 REMARK 3 S31: -0.0782 S32: -0.1883 S33: 0.1563 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 10 REMARK 3 RESIDUE RANGE : F 1 F 10 REMARK 3 ORIGIN FOR THE GROUP (A): -20.5460 43.3600 -12.1760 REMARK 3 T TENSOR REMARK 3 T11: 0.0874 T22: 0.2324 REMARK 3 T33: 0.1759 T12: 0.1814 REMARK 3 T13: 0.0756 T23: 0.0328 REMARK 3 L TENSOR REMARK 3 L11: 2.3527 L22: 4.5193 REMARK 3 L33: 2.3223 L12: -2.2427 REMARK 3 L13: -0.2342 L23: -0.3101 REMARK 3 S TENSOR REMARK 3 S11: -0.2948 S12: -0.0361 S13: 0.0866 REMARK 3 S21: 0.6167 S22: 0.1417 S23: -0.1188 REMARK 3 S31: 0.0430 S32: -0.4644 S33: 0.1531 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AT THE FLANK OF THE RECOGNITION REMARK 3 SEQUENCE SHALLOW INTERCALATION OF AN UNKNOWN MOLECULE IS REMARK 3 SUGGESTED BY ELECTRON DENSITY MAPS. WE HAVE NOT BEEN ABLE TO REMARK 3 DISTINGUISH WHETHER THIS DENSITY SHOULD BE ACCOUNTED FOR BY A REMARK 3 SECOND CONFORMER OF ASN77 OR EITHER B-MERCAPTOETHANOL, ACETATE REMARK 3 OR AZIDE FROM THE BUFFER. THE DESIGNATION OF ONE OF THE IONS AS REMARK 3 NA+ IS TENTATIVE ONLY. PROGRAM CNS HAS BEEN USED FOR DNA REMARK 3 REFINEMENT. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 TLS REFINEMENT HAS BEEN USED. REMARK 4 REMARK 4 4KYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000079968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.23953 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.370 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 20.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.68 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 FOR SHELL : 4.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4ESJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 160 MM CALCIUM ACETATE, 80 MM SODIUM REMARK 280 CACODYLATE PH 6.5, 14.4% W/V PEG 8000, 20% V/V GLYCEROL, 10 MM REMARK 280 SPERMIDINE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 57.42500 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 57.42500 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 47.85000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.52500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.85000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.52500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.42500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.85000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.52500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.42500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.85000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.52500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: BIOLOGICAL UNIT CONTAINS PROTEIN CHAIN A AND TWO DOUBLE REMARK 300 STRANDED DNA FRAGMENTS BOUND TO ITS N- AND C-TERMINAL DOMAINS. TO REMARK 300 THE BEST OF OUR KNOWLEDGE THE OBSERVED COMPLEX CORRESPONDS TO THE REMARK 300 ENZYME SUBSTRATE COMPLEX FORMED BY TYPE IIE R.DPNI RESTRICTION REMARK 300 ENDONUCLEASE AND DOUBLE STRANDED DNA IN SOLUTION. THE PENTAMER REMARK 300 (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE ENZYME WITH TWO REMARK 300 DOUBLE STRANDED DNA FRAGMENTS PRESENT IN THE CRYSTAL. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 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 A 78 -155.14 -141.78 REMARK 500 ASN A 92 44.74 -103.09 REMARK 500 ARG A 135 59.43 -94.76 REMARK 500 ASP A 159 54.77 39.24 REMARK 500 PHE A 220 70.84 -116.18 REMARK 500 HIS A 225 54.64 -142.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT C 6 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ESJ RELATED DB: PDB REMARK 900 RESTRICTION ENDONUCLEASE DPNI IN COMPLEX WITH TARGET DNA DBREF 4KYW A 1 254 UNP P0A459 T2D1_STRPN 1 254 DBREF 4KYW C 1 10 PDB 4KYW 4KYW 1 10 DBREF 4KYW D 1 10 PDB 4KYW 4KYW 1 10 DBREF 4KYW E 1 10 PDB 4KYW 4KYW 1 10 DBREF 4KYW F 1 10 PDB 4KYW 4KYW 1 10 SEQADV 4KYW GLY A -2 UNP P0A459 EXPRESSION TAG SEQADV 4KYW PRO A -1 UNP P0A459 EXPRESSION TAG SEQADV 4KYW HIS A 0 UNP P0A459 EXPRESSION TAG SEQADV 4KYW ASN A 134 UNP P0A459 ARG 134 ENGINEERED MUTATION SEQRES 1 A 257 GLY PRO HIS MET GLU LEU HIS PHE ASN LEU GLU LEU VAL SEQRES 2 A 257 GLU THR TYR LYS SER ASN SER GLN LYS ALA ARG ILE LEU SEQRES 3 A 257 THR GLU ASP TRP VAL TYR ARG GLN SER TYR CYS PRO ASN SEQRES 4 A 257 CYS GLY ASN ASN PRO LEU ASN HIS PHE GLU ASN ASN ARG SEQRES 5 A 257 PRO VAL ALA ASP PHE TYR CYS ASN HIS CYS SER GLU GLU SEQRES 6 A 257 PHE GLU LEU LYS SER LYS LYS GLY ASN PHE SER SER THR SEQRES 7 A 257 ILE ASN ASP GLY ALA TYR ALA THR MET MET LYS ARG VAL SEQRES 8 A 257 GLN ALA ASP ASN ASN PRO ASN PHE PHE PHE LEU THR TYR SEQRES 9 A 257 THR LYS ASN PHE GLU VAL ASN ASN PHE LEU VAL LEU PRO SEQRES 10 A 257 LYS GLN PHE VAL THR PRO LYS SER ILE ILE GLN ARG LYS SEQRES 11 A 257 PRO LEU ALA PRO THR ALA ASN ARG ALA GLY TRP ILE GLY SEQRES 12 A 257 CYS ASN ILE ASP LEU SER GLN VAL PRO SER LYS GLY ARG SEQRES 13 A 257 ILE PHE LEU VAL GLN ASP GLY GLN VAL ARG ASP PRO GLU SEQRES 14 A 257 LYS VAL THR LYS GLU PHE LYS GLN GLY LEU PHE LEU ARG SEQRES 15 A 257 LYS SER SER LEU SER SER ARG GLY TRP THR ILE GLU ILE SEQRES 16 A 257 LEU ASN CYS ILE ASP LYS ILE GLU GLY SER GLU PHE THR SEQRES 17 A 257 LEU GLU ASP MET TYR ARG PHE GLU SER ASP LEU LYS ASN SEQRES 18 A 257 ILE PHE VAL LYS ASN ASN HIS ILE LYS GLU LYS ILE ARG SEQRES 19 A 257 GLN GLN LEU GLN ILE LEU ARG ASP LYS GLU ILE ILE GLU SEQRES 20 A 257 PHE LYS GLY ARG GLY LYS TYR ARG LYS LEU SEQRES 1 C 10 DC DT DG DG 6MA DT DC DC DA DG SEQRES 1 D 10 DC DT DG DG 6MA DT DC DC DA DG SEQRES 1 E 10 DC DT DG DG 6MA DT DC DC DA DG SEQRES 1 F 10 DC DT DG DG 6MA DT DC DC DA DG MODRES 4KYW 6MA C 5 A MODRES 4KYW 6MA D 5 A MODRES 4KYW 6MA E 5 A MODRES 4KYW 6MA F 5 A HET 6MA C 5 22 HET 6MA D 5 22 HET 6MA E 5 22 HET 6MA F 5 22 HET ZN A 301 1 HET CA A 302 1 HET NA A 303 1 HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 6MA 4(C11 H16 N5 O6 P) FORMUL 6 ZN ZN 2+ FORMUL 7 CA CA 2+ FORMUL 8 NA NA 1+ FORMUL 9 HOH *94(H2 O) HELIX 1 1 ASN A 6 GLU A 11 5 6 HELIX 2 2 SER A 15 SER A 32 1 18 HELIX 3 3 TYR A 81 VAL A 88 1 8 HELIX 4 4 PRO A 114 VAL A 118 5 5 HELIX 5 5 THR A 119 LYS A 121 5 3 HELIX 6 6 PRO A 149 ARG A 153 5 5 HELIX 7 7 ASP A 164 LEU A 176 1 13 HELIX 8 8 GLY A 187 ILE A 199 1 13 HELIX 9 9 LEU A 206 TYR A 210 1 5 HELIX 10 10 PHE A 212 PHE A 220 1 9 HELIX 11 11 HIS A 225 LYS A 240 1 16 SHEET 1 A 7 ASN A 43 HIS A 44 0 SHEET 2 A 7 PHE A 54 TYR A 55 -1 O TYR A 55 N ASN A 43 SHEET 3 A 7 GLU A 62 LYS A 69 -1 O PHE A 63 N PHE A 54 SHEET 4 A 7 ASN A 95 TYR A 101 1 O ASN A 95 N GLU A 62 SHEET 5 A 7 VAL A 107 LEU A 113 -1 O ASN A 109 N THR A 100 SHEET 6 A 7 ILE A 154 GLN A 158 -1 O LEU A 156 N PHE A 110 SHEET 7 A 7 GLN A 161 VAL A 162 -1 O GLN A 161 N GLN A 158 SHEET 1 B 3 THR A 75 ALA A 80 0 SHEET 2 B 3 GLY A 140 ASP A 144 -1 O ILE A 143 N ILE A 76 SHEET 3 B 3 ILE A 123 GLN A 125 -1 N ILE A 124 O ASN A 142 SHEET 1 C 3 GLU A 203 THR A 205 0 SHEET 2 C 3 LYS A 250 LYS A 253 -1 O TYR A 251 N PHE A 204 SHEET 3 C 3 ILE A 243 PHE A 245 -1 N GLU A 244 O ARG A 252 LINK O3' DG C 4 P 6MA C 5 1555 1555 1.60 LINK O3' 6MA C 5 P DT C 6 1555 1555 1.61 LINK O3' DG D 4 P 6MA D 5 1555 1555 1.61 LINK O3' 6MA D 5 P DT D 6 1555 1555 1.61 LINK O3' DG E 4 P 6MA E 5 1555 1555 1.61 LINK O3' 6MA E 5 P DT E 6 1555 1555 1.61 LINK O3' DG F 4 P 6MA F 5 1555 1555 1.61 LINK O3' 6MA F 5 P DT F 6 1555 1555 1.61 CISPEP 1 ASN A 40 PRO A 41 0 -2.60 SITE 1 AC1 4 CYS A 34 CYS A 37 CYS A 56 CYS A 59 SITE 1 AC2 6 ASP A 53 GLU A 64 LEU A 65 HOH A 425 SITE 2 AC2 6 HOH A 452 DT C 6 SITE 1 AC3 6 ASP A 53 HOH A 403 HOH A 422 HOH A 443 SITE 2 AC3 6 6MA C 5 DT C 6 CRYST1 95.700 101.050 114.850 90.00 90.00 90.00 C 2 2 21 32 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 0.010449 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008707 0.00000