HEADER HYDROLASE 26-MAR-19 6R64 TITLE N-TERMINAL DOMAIN OF MODIFICATION DEPENDENT ECOKMCRA RESTRICTION TITLE 2 ENDONUCLEASE (NECO) IN COMPLEX WITH C5MCGG 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*CP*(5CM)P*GP*GP*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*CP*(5CM)P*GP*GP*TP*GP*A)-3'); COMPND 13 CHAIN: D, F; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; 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 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_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, SCOMCRA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SLYVKA,E.ZAGORSKAITE,H.CZAPINSKA,G.SASNAUSKAS,M.BOCHTLER REVDAT 4 24-JAN-24 6R64 1 REMARK REVDAT 3 18-DEC-19 6R64 1 JRNL REVDAT 2 27-NOV-19 6R64 1 JRNL REVDAT 1 23-OCT-19 6R64 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. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16786 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 884 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) : 2.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1193 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3580 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 : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.73000 REMARK 3 B22 (A**2) : -1.73000 REMARK 3 B33 (A**2) : 5.62000 REMARK 3 B12 (A**2) : -0.87000 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): 0.492 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.273 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.219 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.193 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3305 ; 0.006 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2656 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4632 ; 1.146 ; 1.752 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6169 ; 1.048 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 5.380 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;33.592 ;23.109 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;12.424 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.898 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3160 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 702 ; 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): 1173 ; 1.306 ; 4.714 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1172 ; 1.306 ; 4.714 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1468 ; 2.258 ; 7.067 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1469 ; 2.257 ; 7.067 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2132 ; 1.894 ; 6.213 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2133 ; 1.894 ; 6.217 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3165 ; 3.299 ; 9.346 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3919 ; 4.943 ;58.927 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3889 ; 4.915 ;58.859 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 6R64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292100604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-18 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 REMARK 200 MONOCHROMATOR : KMC-1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640 REMARK 200 RESOLUTION RANGE LOW (A) : 45.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 16.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.22300 REMARK 200 FOR THE DATA SET : 12.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 16.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.46300 REMARK 200 FOR SHELL : 1.970 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 6GHC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 85.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 8.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NECO IN THE CRYSTALLIZATION BUFFER (20 REMARK 280 MM TRIS-HCL, PH 8.0, 0.1 M NACL, 1 MM EDTA, 2 MM DTT) WAS REMARK 280 CONCENTRATED TO 8.7 MG/ML AND MIXED IN THE 1:1.2 RATIO WITH 10- REMARK 280 MER TCAC5MCGGTTC OLIGONUCLEOTIDE, ANNEALED TO ITS COMPLEMENTARY REMARK 280 GAAC5MCGTGA STRAND. CRYSTALS WERE GROWN BY MIXING 1.8 UL OF THE REMARK 280 PROTEIN-DNA MIXTURE WITH 2.2 UL OF THE CONDITION F1 OF THE PACT REMARK 280 PREMIER CRYSTAL SCREEN (MDL) (0.2 M NAF, 0.1 M BIS-TRIS PROPANE, REMARK 280 PH 6.5, 20% PEG3350). CRYSTALS WERE CRYO-PROTECTED BY THE REMARK 280 ADDITION OF 25% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 51.81900 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 103.63800 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 77.72850 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 129.54750 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 25.90950 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 51.81900 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 103.63800 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 129.54750 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 77.72850 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 25.90950 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 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 87.92 -160.94 REMARK 500 ALA B 13 88.98 -157.92 REMARK 500 SER B 108 -169.67 -109.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FULL LENGTH ECOKMCRA IN THE ABSENCE OF DNA 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 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 6R64 A 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6R64 B 1 143 UNP P24200 MCRA_ECOLI 1 143 DBREF 6R64 C 1 10 PDB 6R64 6R64 1 10 DBREF 6R64 D 1 10 PDB 6R64 6R64 1 10 DBREF 6R64 E 1 10 PDB 6R64 6R64 1 10 DBREF 6R64 F 1 10 PDB 6R64 6R64 1 10 SEQADV 6R64 GLY A -8 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -7 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -6 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -5 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -4 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -3 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS A -2 UNP P24200 EXPRESSION TAG SEQADV 6R64 GLU A -1 UNP P24200 EXPRESSION TAG SEQADV 6R64 PHE A 0 UNP P24200 EXPRESSION TAG SEQADV 6R64 GLY B -8 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -7 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -6 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -5 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -4 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -3 UNP P24200 EXPRESSION TAG SEQADV 6R64 HIS B -2 UNP P24200 EXPRESSION TAG SEQADV 6R64 GLU B -1 UNP P24200 EXPRESSION TAG SEQADV 6R64 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 DC 5CM DG DG DT DT DC SEQRES 1 D 10 DG DA DA DC 5CM DG DG DT DG DA SEQRES 1 E 10 DT DC DA DC 5CM DG DG DT DT DC SEQRES 1 F 10 DG DA DA DC 5CM DG DG 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 *146(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 CYS A 15 N MET A 1 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' DC 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' DC D 4 P 5CM D 5 1555 1555 1.60 LINK O3' 5CM D 5 P DG D 6 1555 1555 1.60 LINK O3' DC E 4 P 5CM E 5 1555 1555 1.60 LINK O3' 5CM E 5 P DG E 6 1555 1555 1.60 LINK O3' DC F 4 P 5CM F 5 1555 1555 1.60 LINK O3' 5CM F 5 P DG F 6 1555 1555 1.61 CISPEP 1 GLY A 32 PRO A 33 0 1.22 CISPEP 2 GLY B 32 PRO B 33 0 -0.77 CRYST1 112.432 112.432 155.457 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 0.008894 0.005135 0.000000 0.00000 SCALE2 0.000000 0.010270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006433 0.00000