HEADER HYDROLASE 07-OCT-19 6T22 TITLE N-TERMINAL DOMAIN OF ECOKMCRA RESTRICTION ENDONUCLEASE (NECO) IN TITLE 2 COMPLEX WITH T5HMCGA TARGET SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECOKMCRA MODIFICATION DEPENDENT RESTRICTION ENDONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.21.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*CP*AP*TP*(5HC)P*GP*AP*TP*TP*C)-3'); COMPND 8 CHAIN: C, E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*(5HC)P*GP*AP*TP*GP*A)-3'); COMPND 12 CHAIN: D, F; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: MCRA, RGLA, B1159, JW1145; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15BM; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS ECOKMCRA, NECO, N-TERMINAL DOMAIN, MODIFICATION DEPENDENT KEYWDS 2 RESTRICTION, 5-METHYLCYTOSINE, 5MC, 5-HYDROXYMETHYLCYTOSINE, 5HMC, KEYWDS 3 HNH ENDONUCLEASE, BBA-ME NUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SLYVKA,E.ZAGORSKAITE,H.CZAPINSKA,G.SASNAUSKAS,M.BOCHTLER REVDAT 4 24-JAN-24 6T22 1 REMARK REVDAT 3 18-DEC-19 6T22 1 JRNL REVDAT 2 27-NOV-19 6T22 1 JRNL REVDAT 1 30-OCT-19 6T22 0 JRNL AUTH A.SLYVKA,E.ZAGORSKAITE,H.CZAPINSKA,G.SASNAUSKAS,M.BOCHTLER JRNL TITL CRYSTAL STRUCTURE OF THE ECOKMCRA N-TERMINAL DOMAIN (NECO): JRNL TITL 2 RECOGNITION OF MODIFIED CYTOSINE BASES WITHOUT FLIPPING. JRNL REF NUCLEIC ACIDS RES. V. 47 11943 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31724709 JRNL DOI 10.1093/NAR/GKZ1017 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.CZAPINSKA,M.KOWALSKA,E.ZAGORSKAITE,E.MANAKOVA,A.SLYVKA, REMARK 1 AUTH 2 S.Y.XU,V.SIKSNYS,G.SASNAUSKAS,M.BOCHTLER REMARK 1 TITL ACTIVITY AND STRUCTURE OF ECOKMCRA. REMARK 1 REF NUCLEIC ACIDS RES. V. 46 9829 2018 REMARK 1 REFN ESSN 1362-4962 REMARK 1 PMID 30107581 REMARK 1 DOI 10.1093/NAR/GKY731 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 28708 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1534 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1945 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2320 REMARK 3 NUCLEIC ACID ATOMS : 816 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.31000 REMARK 3 B33 (A**2) : 1.01000 REMARK 3 B12 (A**2) : -0.16000 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): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.998 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3399 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2758 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4767 ; 1.210 ; 1.548 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6424 ; 1.294 ; 1.832 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 6.284 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;32.341 ;20.759 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 446 ;12.540 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;13.773 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3348 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 748 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 -5 A 145 REMARK 3 RESIDUE RANGE : C 1 C 10 REMARK 3 RESIDUE RANGE : D 1 D 10 REMARK 3 ORIGIN FOR THE GROUP (A): -16.5228 29.2994 -6.4928 REMARK 3 T TENSOR REMARK 3 T11: 0.0509 T22: 0.0758 REMARK 3 T33: 0.1086 T12: 0.0410 REMARK 3 T13: -0.0347 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 1.5009 L22: 2.3651 REMARK 3 L33: 0.7662 L12: 0.7803 REMARK 3 L13: 1.0197 L23: 0.1926 REMARK 3 S TENSOR REMARK 3 S11: 0.0957 S12: 0.2000 S13: -0.2733 REMARK 3 S21: 0.3041 S22: 0.1513 S23: -0.0972 REMARK 3 S31: 0.0454 S32: 0.1016 S33: -0.2470 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -5 B 145 REMARK 3 RESIDUE RANGE : E 1 E 10 REMARK 3 RESIDUE RANGE : F 1 F 10 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1498 51.7371 5.8043 REMARK 3 T TENSOR REMARK 3 T11: 0.1304 T22: 0.0531 REMARK 3 T33: 0.0461 T12: 0.0036 REMARK 3 T13: -0.0531 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.4861 L22: 1.5722 REMARK 3 L33: 1.2067 L12: 0.9116 REMARK 3 L13: -0.4008 L23: -0.4792 REMARK 3 S TENSOR REMARK 3 S11: 0.2769 S12: 0.0833 S13: 0.0178 REMARK 3 S21: 0.3407 S22: -0.1465 S23: -0.0809 REMARK 3 S31: -0.0039 S32: 0.0147 S33: -0.1304 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 TLS REFINEMENT HAS BEEN USED. REMARK 3 U VALUES : WITH TLS ADDED. REMARK 3 THE CLUSTERS OF SOLVENT MOLECULES BETWEEN RESIDUES 46 AND 94 AND REMARK 3 NEXT TO RESIDUE 54 OF CHAIN B LIKELY CORRESPOND TO DISORDERED REMARK 3 GLYCEROL MOLECULES. THE ELECTRON DENSITY IS NOT DEFINED ENOUGH TO REMARK 3 UNAMBIGUOUSLY MODEL THEM. REMARK 4 REMARK 4 6T22 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.9195 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30298 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 33.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 35.80 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 20.80 REMARK 200 R MERGE FOR SHELL (I) : 1.76100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 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: 6GHC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 UL OF PROTEIN-DNA SOLUTION REMARK 280 (436:523 UM) WAS MIXED WITH 2.2 UL OF THE F1 CONDITION OF THE REMARK 280 PACT PREMIER CRYSTAL SCREEN (MDL) (0.2 M SODIUM FLUORIDE, 0.1 M REMARK 280 BIS-TRIS PROPANE, PH 6.5, 20% PEG 3350) AND CRYO-PROTECTED WITH REMARK 280 AN ADDITION OF 25% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.12233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.24467 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 78.18350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 130.30583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.06117 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.12233 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 104.24467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 130.30583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 78.18350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.06117 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 350 REMARK 350 BIOMOLECULE: 2 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: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 323 LIES ON A SPECIAL POSITION. 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 -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 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 ALA A 13 88.10 -155.87 REMARK 500 SER B 108 -169.19 -102.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 344 DISTANCE = 5.96 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FULL-LENGTH DIMERIC ECOKMCRA RESTRICTION REMARK 900 ENDONUCLEASE REMARK 900 RELATED ID: 6R64 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N-TERMINAL (NECO) DOMAIN OF ECOKMCRA IN REMARK 900 COMPLEX WITH C5MCGG TARGET SEQUENCE REMARK 900 RELATED ID: 6T21 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF ECOKMCRA RESTRICTION REMARK 900 ENDONUCLEASE (NECO) IN COMPLEX WITH T5MCGA TARGET SEQUENCE DBREF 6T22 A 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6T22 B 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6T22 C 1 10 PDB 6T22 6T22 1 10 DBREF 6T22 D 1 10 PDB 6T22 6T22 1 10 DBREF 6T22 E 1 10 PDB 6T22 6T22 1 10 DBREF 6T22 F 1 10 PDB 6T22 6T22 1 10 SEQADV 6T22 GLY A -8 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -7 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -6 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -5 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -4 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -3 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS A -2 UNP P24200 EXPRESSION TAG SEQADV 6T22 GLU A -1 UNP P24200 EXPRESSION TAG SEQADV 6T22 PHE A 0 UNP P24200 EXPRESSION TAG SEQADV 6T22 GLY B -8 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -7 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -6 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -5 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -4 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -3 UNP P24200 EXPRESSION TAG SEQADV 6T22 HIS B -2 UNP P24200 EXPRESSION TAG SEQADV 6T22 GLU B -1 UNP P24200 EXPRESSION TAG SEQADV 6T22 PHE B 0 UNP P24200 EXPRESSION TAG SEQRES 1 A 152 GLY HIS HIS HIS HIS HIS HIS GLU PHE MET HIS VAL PHE SEQRES 2 A 152 ASP ASN ASN GLY ILE GLU LEU LYS ALA GLU CYS SER ILE SEQRES 3 A 152 GLY GLU GLU ASP GLY VAL TYR GLY LEU ILE LEU GLU SER SEQRES 4 A 152 TRP GLY PRO GLY ASP ARG ASN LYS ASP TYR ASN ILE ALA SEQRES 5 A 152 LEU ASP TYR ILE ILE GLU ARG LEU VAL ASP SER GLY VAL SEQRES 6 A 152 SER GLN VAL VAL VAL TYR LEU ALA SER SER SER VAL ARG SEQRES 7 A 152 LYS HIS MET HIS SER LEU ASP GLU ARG LYS ILE HIS PRO SEQRES 8 A 152 GLY GLU TYR PHE THR LEU ILE GLY ASN SER PRO ARG ASP SEQRES 9 A 152 ILE ARG LEU LYS MET CYS GLY TYR GLN ALA TYR PHE SER SEQRES 10 A 152 ARG THR GLY ARG LYS GLU ILE PRO SER GLY ASN ARG THR SEQRES 11 A 152 LYS ARG ILE LEU ILE ASN VAL PRO GLY ILE TYR SER ASP SEQRES 12 A 152 SER PHE TRP ALA SER ILE ILE ARG GLY SEQRES 1 B 152 GLY HIS HIS HIS HIS HIS HIS GLU PHE MET HIS VAL PHE SEQRES 2 B 152 ASP ASN ASN GLY ILE GLU LEU LYS ALA GLU CYS SER ILE SEQRES 3 B 152 GLY GLU GLU ASP GLY VAL TYR GLY LEU ILE LEU GLU SER SEQRES 4 B 152 TRP GLY PRO GLY ASP ARG ASN LYS ASP TYR ASN ILE ALA SEQRES 5 B 152 LEU ASP TYR ILE ILE GLU ARG LEU VAL ASP SER GLY VAL SEQRES 6 B 152 SER GLN VAL VAL VAL TYR LEU ALA SER SER SER VAL ARG SEQRES 7 B 152 LYS HIS MET HIS SER LEU ASP GLU ARG LYS ILE HIS PRO SEQRES 8 B 152 GLY GLU TYR PHE THR LEU ILE GLY ASN SER PRO ARG ASP SEQRES 9 B 152 ILE ARG LEU LYS MET CYS GLY TYR GLN ALA TYR PHE SER SEQRES 10 B 152 ARG THR GLY ARG LYS GLU ILE PRO SER GLY ASN ARG THR SEQRES 11 B 152 LYS ARG ILE LEU ILE ASN VAL PRO GLY ILE TYR SER ASP SEQRES 12 B 152 SER PHE TRP ALA SER ILE ILE ARG GLY SEQRES 1 C 10 DT DC DA DT 5HC DG DA DT DT DC SEQRES 1 D 10 DG DA DA DT 5HC DG DA DT DG DA SEQRES 1 E 10 DT DC DA DT 5HC DG DA DT DT DC SEQRES 1 F 10 DG DA DA DT 5HC DG DA DT DG DA HET 5HC C 5 21 HET 5HC D 5 21 HET 5HC E 5 21 HET 5HC F 5 21 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 3 5HC 4(C10 H16 N3 O8 P) FORMUL 7 HOH *405(H2 O) HELIX 1 AA1 ASP A 39 SER A 54 1 16 HELIX 2 AA2 SER A 65 MET A 72 1 8 HELIX 3 AA3 SER A 74 LYS A 79 1 6 HELIX 4 AA4 SER A 92 TYR A 103 1 12 HELIX 5 AA5 GLN A 104 PHE A 107 5 4 HELIX 6 AA6 SER A 133 GLY A 143 1 11 HELIX 7 AA7 ASP B 39 SER B 54 1 16 HELIX 8 AA8 SER B 65 MET B 72 1 8 HELIX 9 AA9 SER B 74 LYS B 79 1 6 HELIX 10 AB1 SER B 92 TYR B 103 1 12 HELIX 11 AB2 GLN B 104 PHE B 107 5 4 HELIX 12 AB3 SER B 133 GLY B 143 1 11 SHEET 1 AA1 6 MET A 1 PHE A 4 0 SHEET 2 AA1 6 GLU A 10 GLU A 20 -1 O LEU A 11 N VAL A 3 SHEET 3 AA1 6 VAL A 23 LEU A 28 -1 O ILE A 27 N SER A 16 SHEET 4 AA1 6 ILE A 124 ASN A 127 -1 O ILE A 126 N LEU A 26 SHEET 5 AA1 6 GLN A 58 LEU A 63 -1 N VAL A 60 O ASN A 127 SHEET 6 AA1 6 PHE A 86 THR A 87 -1 O PHE A 86 N VAL A 59 SHEET 1 AA2 6 MET B 1 PHE B 4 0 SHEET 2 AA2 6 GLU B 10 GLU B 20 -1 O LEU B 11 N VAL B 3 SHEET 3 AA2 6 VAL B 23 LEU B 28 -1 O ILE B 27 N SER B 16 SHEET 4 AA2 6 ILE B 124 ASN B 127 -1 O ILE B 126 N LEU B 26 SHEET 5 AA2 6 GLN B 58 LEU B 63 -1 N VAL B 60 O ASN B 127 SHEET 6 AA2 6 PHE B 86 THR B 87 -1 O PHE B 86 N VAL B 59 LINK O3' DT C 4 P 5HC C 5 1555 1555 1.59 LINK O3' 5HC C 5 P DG C 6 1555 1555 1.60 LINK O3' DT D 4 P 5HC D 5 1555 1555 1.58 LINK O3' 5HC D 5 P DG D 6 1555 1555 1.60 LINK O3' DT E 4 P 5HC E 5 1555 1555 1.59 LINK O3' 5HC E 5 P DG E 6 1555 1555 1.60 LINK O3' DT F 4 P 5HC F 5 1555 1555 1.60 LINK O3' 5HC F 5 P DG F 6 1555 1555 1.61 CISPEP 1 GLY A 32 PRO A 33 0 -4.42 CISPEP 2 GLY B 32 PRO B 33 0 -5.53 CRYST1 113.417 113.417 156.367 90.00 90.00 120.00 P 61 2 2 24 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 0.008817 0.005091 0.000000 0.00000 SCALE2 0.000000 0.010181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006395 0.00000