HEADER HYDROLASE 07-OCT-19 6T21 TITLE N-TERMINAL DOMAIN OF ECOKMCRA RESTRICTION ENDONUCLEASE (NECO) IN TITLE 2 COMPLEX WITH T5MCGA TARGET SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-METHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ECOKMCRA; COMPND 5 EC: 3.1.21.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*CP*AP*TP*(5CM)P*GP*AP*TP*TP*C)-3'); COMPND 9 CHAIN: C, E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*(5CM)P*GP*AP*TP*GP*A)-3'); COMPND 13 CHAIN: D, F; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: MCRA, RGLA, B1159, JW1145; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15BM; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 19 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 6T21 1 REMARK REVDAT 3 18-DEC-19 6T21 1 JRNL REVDAT 2 27-NOV-19 6T21 1 JRNL REVDAT 1 23-OCT-19 6T21 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. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 34065 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1824 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2124 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2320 REMARK 3 NUCLEIC ACID ATOMS : 812 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 431 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.99000 REMARK 3 B12 (A**2) : -0.15000 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): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.669 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3461 ; 0.006 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2818 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4853 ; 1.152 ; 1.768 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6567 ; 0.920 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 5.197 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;35.061 ;22.960 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 461 ;11.638 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;13.552 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 476 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3439 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 758 ; 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 -1 A 143 REMARK 3 RESIDUE RANGE : C 1 C 10 REMARK 3 RESIDUE RANGE : D 1 D 10 REMARK 3 ORIGIN FOR THE GROUP (A): -16.0796 28.8253 -6.3212 REMARK 3 T TENSOR REMARK 3 T11: 0.0503 T22: 0.0319 REMARK 3 T33: 0.1062 T12: 0.0239 REMARK 3 T13: -0.0236 T23: -0.0504 REMARK 3 L TENSOR REMARK 3 L11: 1.7791 L22: 1.7135 REMARK 3 L33: 0.4966 L12: 0.9519 REMARK 3 L13: 0.9213 L23: 0.3497 REMARK 3 S TENSOR REMARK 3 S11: 0.1590 S12: 0.1771 S13: -0.3897 REMARK 3 S21: 0.2260 S22: 0.0657 S23: -0.1015 REMARK 3 S31: 0.0637 S32: 0.0925 S33: -0.2247 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 -1 B 143 REMARK 3 RESIDUE RANGE : E 1 E 10 REMARK 3 RESIDUE RANGE : F 1 F 10 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4127 51.5266 5.9053 REMARK 3 T TENSOR REMARK 3 T11: 0.1174 T22: 0.0286 REMARK 3 T33: 0.0214 T12: -0.0019 REMARK 3 T13: -0.0411 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.5429 L22: 1.3201 REMARK 3 L33: 0.6344 L12: 0.9161 REMARK 3 L13: -0.3105 L23: 0.0471 REMARK 3 S TENSOR REMARK 3 S11: 0.1845 S12: -0.0261 S13: -0.0659 REMARK 3 S21: 0.3153 S22: -0.1107 S23: -0.1034 REMARK 3 S31: 0.0461 S32: -0.0056 S33: -0.0737 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 HYDROGENS 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 6T21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-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) : 0.9793 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 : 36261 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 33.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 38.87 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 38.92 REMARK 200 R MERGE FOR SHELL (I) : 2.29900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.980 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: 6R64 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 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 51.91700 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 103.83400 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 77.87550 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 129.79250 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 25.95850 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 51.91700 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 103.83400 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 129.79250 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 77.87550 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 25.95850 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 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 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 340 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: 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 5CM F 5 O3' - P - OP2 ANGL. DEV. = 9.4 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 SER A 108 -168.76 -101.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GHC RELATED DB: PDB REMARK 900 MODIFICATION DEPENDENT ECOKMCRA RESTRICTION ENDONUCLEASE REMARK 900 RELATED ID: 6R64 RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF ECOKMCRA IN COMPLEX WITH C5MCGG TARGET REMARK 900 SEQUENCE. REMARK 900 RELATED ID: 6T22 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF ECOKMCRA RESTRICTION REMARK 900 ENDONUCLEASE (NECO) IN COMPLEX WITH T5HMCGA TARGET SEQUENCE DBREF 6T21 A 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6T21 B 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6T21 C 1 10 PDB 6T21 6T21 1 10 DBREF 6T21 D 1 10 PDB 6T21 6T21 1 10 DBREF 6T21 E 1 10 PDB 6T21 6T21 1 10 DBREF 6T21 F 1 10 PDB 6T21 6T21 1 10 SEQADV 6T21 GLY A -8 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -7 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -6 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -5 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -4 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -3 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS A -2 UNP P24200 EXPRESSION TAG SEQADV 6T21 GLU A -1 UNP P24200 EXPRESSION TAG SEQADV 6T21 PHE A 0 UNP P24200 EXPRESSION TAG SEQADV 6T21 GLY B -8 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -7 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -6 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -5 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -4 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -3 UNP P24200 EXPRESSION TAG SEQADV 6T21 HIS B -2 UNP P24200 EXPRESSION TAG SEQADV 6T21 GLU B -1 UNP P24200 EXPRESSION TAG SEQADV 6T21 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 5CM DG DA DT DT DC SEQRES 1 D 10 DG DA DA DT 5CM DG DA DT DG DA SEQRES 1 E 10 DT DC DA DT 5CM DG DA DT DT DC SEQRES 1 F 10 DG DA DA DT 5CM DG DA DT DG DA HET 5CM C 5 20 HET 5CM D 5 20 HET 5CM E 5 20 HET 5CM F 5 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 7 HOH *431(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 5CM C 5 1555 1555 1.60 LINK O3' 5CM C 5 P DG C 6 1555 1555 1.59 LINK O3' DT D 4 P 5CM D 5 1555 1555 1.58 LINK O3' 5CM D 5 P DG D 6 1555 1555 1.60 LINK O3' DT E 4 P 5CM E 5 1555 1555 1.58 LINK O3' 5CM E 5 P DG E 6 1555 1555 1.60 LINK O3' DT F 4 P 5CM F 5 1555 1555 1.59 LINK O3' 5CM F 5 P DG F 6 1555 1555 1.61 CISPEP 1 GLY A 32 PRO A 33 0 -5.32 CISPEP 2 GLY B 32 PRO B 33 0 -7.87 CRYST1 112.882 112.882 155.751 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 0.008859 0.005115 0.000000 0.00000 SCALE2 0.000000 0.010229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006421 0.00000