HEADER HYDROLASE 08-APR-20 6YMG TITLE VCAM4I RESTRICTION ENDONUCLEASE IN COMPLEX WITH 5MC-MODIFIED DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNH ENDONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*A)-3'); COMPND 7 CHAIN: C, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'); COMPND 11 CHAIN: D, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CAMPBELLII; SOURCE 3 ORGANISM_TAXID: 680; SOURCE 4 GENE: DSB67_20905; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTXB1 (MODIFIED); 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 PUA SUPERFAMILY, EVE DOMAIN, DNA ENDONUCLEASE, MODIFICATION-DEPENDENT KEYWDS 2 RESTRICTION ENDONUCLEASE, MDRE, 5-HYDROXYMETHYLCYTOSINE, 5- KEYWDS 3 METHYLCYTOSINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PASTOR,H.CZAPINSKA,T.LUTZ,I.HELBRECHT,S.XU,M.BOCHTLER REVDAT 4 24-JAN-24 6YMG 1 REMARK REVDAT 3 03-MAR-21 6YMG 1 JRNL REVDAT 2 27-JAN-21 6YMG 1 JRNL REVDAT 1 23-DEC-20 6YMG 0 JRNL AUTH M.PASTOR,H.CZAPINSKA,I.HELBRECHT,K.KRAKOWSKA,T.LUTZ,S.Y.XU, JRNL AUTH 2 M.BOCHTLER JRNL TITL CRYSTAL STRUCTURES OF THE EVE-HNH ENDONUCLEASE VCAM4I IN THE JRNL TITL 2 PRESENCE AND ABSENCE OF DNA. JRNL REF NUCLEIC ACIDS RES. V. 49 1708 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33450012 JRNL DOI 10.1093/NAR/GKAA1218 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.LUTZ,K.FLODMAN,A.COPELAS,H.CZAPINSKA,M.MABUCHI,A.FOMENKOV, REMARK 1 AUTH 2 X.HE,M.BOCHTLER,S.Y.XU REMARK 1 TITL A PROTEIN ARCHITECTURE GUIDED SCREEN FOR MODIFICATION REMARK 1 TITL 2 DEPENDENT RESTRICTION ENDONUCLEASES. REMARK 1 REF NUCLEIC ACIDS RES. V. 47 9761 2019 REMARK 1 REFN ESSN 1362-4962 REMARK 1 PMID 31504772 REMARK 1 DOI 10.1093/NAR/GKZ755 REMARK 2 REMARK 2 RESOLUTION. 3.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 3.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 19843 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1031 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) : 3.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2214 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.3870 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4998 REMARK 3 NUCLEIC ACID ATOMS : 892 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : -0.76000 REMARK 3 B33 (A**2) : 2.47000 REMARK 3 B12 (A**2) : -0.38000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.482 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.464 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 65.356 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6203 ; 0.003 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5057 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8587 ; 1.193 ; 1.560 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11807 ; 1.173 ; 1.717 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 621 ; 7.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;34.543 ;23.805 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 881 ;13.924 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;11.394 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 772 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6397 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1335 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 309 B 1 309 10295 0.070 0.050 REMARK 3 2 C 1 11 E 1 11 748 0.130 0.050 REMARK 3 3 D 1 11 F 1 11 879 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 157 A 310 REMARK 3 RESIDUE RANGE : B 157 B 310 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3098 -32.1837 19.9641 REMARK 3 T TENSOR REMARK 3 T11: 0.1986 T22: 0.1648 REMARK 3 T33: 0.0530 T12: -0.0054 REMARK 3 T13: 0.0279 T23: -0.0760 REMARK 3 L TENSOR REMARK 3 L11: 0.6748 L22: 0.1630 REMARK 3 L33: 0.7030 L12: 0.3055 REMARK 3 L13: 0.0653 L23: 0.1568 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: 0.0476 S13: -0.1072 REMARK 3 S21: -0.0200 S22: 0.0195 S23: -0.0471 REMARK 3 S31: -0.1800 S32: 0.0750 S33: -0.0423 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 : A 1 A 156 REMARK 3 RESIDUE RANGE : C 1 C 11 REMARK 3 RESIDUE RANGE : D 1 D 11 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8412 -24.9280 53.1742 REMARK 3 T TENSOR REMARK 3 T11: 0.1573 T22: 0.0949 REMARK 3 T33: 0.0388 T12: -0.0025 REMARK 3 T13: 0.0271 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.2566 L22: 0.5755 REMARK 3 L33: 1.1066 L12: -0.5159 REMARK 3 L13: -0.0194 L23: 0.6249 REMARK 3 S TENSOR REMARK 3 S11: -0.0543 S12: -0.0561 S13: -0.0903 REMARK 3 S21: 0.0208 S22: 0.0488 S23: 0.0243 REMARK 3 S31: -0.0082 S32: 0.0836 S33: 0.0055 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 156 REMARK 3 RESIDUE RANGE : E 1 E 11 REMARK 3 RESIDUE RANGE : F 1 F 11 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8070 -18.4713 -12.0967 REMARK 3 T TENSOR REMARK 3 T11: 0.1096 T22: 0.2042 REMARK 3 T33: 0.0264 T12: 0.0264 REMARK 3 T13: -0.0177 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.6692 L22: 2.2556 REMARK 3 L33: 1.2299 L12: 0.2309 REMARK 3 L13: -0.2855 L23: -0.9901 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: 0.0693 S13: -0.0687 REMARK 3 S21: 0.1326 S22: -0.1245 S23: 0.0319 REMARK 3 S31: -0.0876 S32: 0.0564 S33: 0.1139 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 U VALUES : WITH TLS ADDED. THE IDENTITY OF THE SOLVENT REMARK 3 MOLECULES HAS BEEN ASSIGNED TENTATIVELY. REMARK 4 REMARK 4 6YMG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.25 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) : 0.9184 REMARK 200 MONOCHROMATOR : NULL 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 : 20874 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.140 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.21500 REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.52100 REMARK 200 FOR SHELL : 0.890 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: 6YEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 1.2 M (NH4)2SO4 , REMARK 280 0.1 M MES PH 5.25; PROTEIN:DNA SOLUTION: 0.3 M NACL, 15 MM TRIS- REMARK 280 HCL PH 8.5 AND 1 MM TCEP. FOR CRYO-PROTECTION THE RESERVOIR REMARK 280 SOLUTION WAS DILUTED WITH GLYCEROL TO ACHIEVE 30% CONCENTRATION., REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 205.76900 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 411.53800 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 308.65350 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 514.42250 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 102.88450 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 205.76900 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 411.53800 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 514.42250 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 308.65350 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 102.88450 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 S SO4 A 404 LIES ON A SPECIAL POSITION. 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 THR A 11 29.36 -140.38 REMARK 500 GLU A 92 91.78 -69.23 REMARK 500 ILE A 154 -71.77 -95.00 REMARK 500 PHE A 157 -89.62 -145.84 REMARK 500 ILE A 225 -69.74 -91.88 REMARK 500 ASN A 241 54.08 -95.51 REMARK 500 THR B 11 30.07 -144.25 REMARK 500 ALA B 83 150.75 -48.78 REMARK 500 GLU B 92 91.27 -69.11 REMARK 500 ILE B 154 -71.78 -93.40 REMARK 500 PHE B 157 -90.34 -145.84 REMARK 500 ILE B 225 -69.20 -91.95 REMARK 500 ASN B 241 53.47 -95.53 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 CL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DG E 5 and 5CM E REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM E 6 and DG E REMARK 800 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5J3E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYN1 PROTEIN IN COMPLEX WITH 5- REMARK 900 METHYLCYTOSINE CONTAINING DNA REMARK 900 RELATED ID: 6YEX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VCAM4I RESTRICTION ENDONUCLEASE IN THE ABSENCE REMARK 900 OF DNA REMARK 900 RELATED ID: 6YJB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VCAM4I RESTRICTION ENDONUCLEASE IN THE REMARK 900 PRESENCE OF 5HMC-MODIFIED SSDNA REMARK 900 RELATED ID: 6YKF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VCAM4I RESTRICTION ENDONUCLEASE IN THE REMARK 900 PRESENCE OF 5MC-MODIFIED SSDNA DBREF1 6YMG A 1 309 UNP A0A344KQF3_9VIBR DBREF2 6YMG A A0A344KQF3 1 309 DBREF1 6YMG B 1 309 UNP A0A344KQF3_9VIBR DBREF2 6YMG B A0A344KQF3 1 309 DBREF 6YMG C 1 11 PDB 6YMG 6YMG 1 11 DBREF 6YMG D 1 11 PDB 6YMG 6YMG 1 11 DBREF 6YMG E 1 11 PDB 6YMG 6YMG 1 11 DBREF 6YMG F 1 11 PDB 6YMG 6YMG 1 11 SEQRES 1 A 309 MET ASN TYR TRP TRP VAL SER GLN LYS GLN THR PHE LYS SEQRES 2 A 309 GLN GLU PHE GLU GLY GLY TYR MET TRP SER PRO LYS GLU SEQRES 3 A 309 ASN LYS ASN GLY THR GLN SER HIS TYR TYR ASN ASN MET SEQRES 4 A 309 THR LEU VAL GLN PRO GLY ASP VAL VAL PHE SER PHE ALA SEQRES 5 A 309 ASN GLY LEU ILE LEU SER VAL GLY ILE ALA ARG SER HIS SEQRES 6 A 309 ALA TYR SER TYR ASN LYS PRO THR GLU PHE GLY VAL ALA SEQRES 7 A 309 GLY ALA ASP TRP ALA ASN ASP GLY TRP LYS ILE ASP LEU SEQRES 8 A 309 GLU TYR HIS LEU VAL GLU ASN LYS ILE ARG PRO LYS ALA SEQRES 9 A 309 HIS ILE ASP PHE ILE ARG PRO TYR LEU PRO GLN LYS TYR SEQRES 10 A 309 SER PRO LEU GLN ASP ASN GLY ASN GLY ASN GLN ALA TYR SEQRES 11 A 309 LEU PHE SER VAL PRO HIS GLU LEU ALA SER LYS VAL VAL SEQRES 12 A 309 GLU LEU ILE GLY SER GLU ALA GLU GLU VAL ILE PHE GLY SEQRES 13 A 309 PHE ALA ASP THR THR GLU ILE THR THR THR ALA ASP ALA SEQRES 14 A 309 ILE GLU CYS GLN ILE SER ASN ASP ALA SER ILE ASP GLU SEQRES 15 A 309 THR GLU LYS HIS GLN LEU VAL LYS SER ARG ARG GLY GLN SEQRES 16 A 309 GLY ILE PHE ARG SER ARG LEU GLU GLN VAL GLU SER ARG SEQRES 17 A 309 CYS ARG VAL THR GLY VAL GLN LEU LYS ASN HIS LEU ILE SEQRES 18 A 309 ALA SER HIS ILE LYS PRO TRP ALA VAL SER ASN ASN GLN SEQRES 19 A 309 GLU ARG LEU ASP GLY HIS ASN GLY LEU LEU LEU ALA PRO SEQRES 20 A 309 HIS VAL ASP HIS LEU PHE ASP LYS GLY PHE ILE SER PHE SEQRES 21 A 309 GLU ASP ASN GLY GLU MET ILE VAL SER GLU LYS LEU ASN SEQRES 22 A 309 LEU ASP VAL LEU LYS ALA TRP SER ILE SER GLN GLY ASN SEQRES 23 A 309 TYR GLY TYR PHE SER LYS GLN GLN GLN GLU TYR MET CYS SEQRES 24 A 309 TYR HIS ARG GLU ASN VAL PHE LYS LYS LEU SEQRES 1 B 309 MET ASN TYR TRP TRP VAL SER GLN LYS GLN THR PHE LYS SEQRES 2 B 309 GLN GLU PHE GLU GLY GLY TYR MET TRP SER PRO LYS GLU SEQRES 3 B 309 ASN LYS ASN GLY THR GLN SER HIS TYR TYR ASN ASN MET SEQRES 4 B 309 THR LEU VAL GLN PRO GLY ASP VAL VAL PHE SER PHE ALA SEQRES 5 B 309 ASN GLY LEU ILE LEU SER VAL GLY ILE ALA ARG SER HIS SEQRES 6 B 309 ALA TYR SER TYR ASN LYS PRO THR GLU PHE GLY VAL ALA SEQRES 7 B 309 GLY ALA ASP TRP ALA ASN ASP GLY TRP LYS ILE ASP LEU SEQRES 8 B 309 GLU TYR HIS LEU VAL GLU ASN LYS ILE ARG PRO LYS ALA SEQRES 9 B 309 HIS ILE ASP PHE ILE ARG PRO TYR LEU PRO GLN LYS TYR SEQRES 10 B 309 SER PRO LEU GLN ASP ASN GLY ASN GLY ASN GLN ALA TYR SEQRES 11 B 309 LEU PHE SER VAL PRO HIS GLU LEU ALA SER LYS VAL VAL SEQRES 12 B 309 GLU LEU ILE GLY SER GLU ALA GLU GLU VAL ILE PHE GLY SEQRES 13 B 309 PHE ALA ASP THR THR GLU ILE THR THR THR ALA ASP ALA SEQRES 14 B 309 ILE GLU CYS GLN ILE SER ASN ASP ALA SER ILE ASP GLU SEQRES 15 B 309 THR GLU LYS HIS GLN LEU VAL LYS SER ARG ARG GLY GLN SEQRES 16 B 309 GLY ILE PHE ARG SER ARG LEU GLU GLN VAL GLU SER ARG SEQRES 17 B 309 CYS ARG VAL THR GLY VAL GLN LEU LYS ASN HIS LEU ILE SEQRES 18 B 309 ALA SER HIS ILE LYS PRO TRP ALA VAL SER ASN ASN GLN SEQRES 19 B 309 GLU ARG LEU ASP GLY HIS ASN GLY LEU LEU LEU ALA PRO SEQRES 20 B 309 HIS VAL ASP HIS LEU PHE ASP LYS GLY PHE ILE SER PHE SEQRES 21 B 309 GLU ASP ASN GLY GLU MET ILE VAL SER GLU LYS LEU ASN SEQRES 22 B 309 LEU ASP VAL LEU LYS ALA TRP SER ILE SER GLN GLY ASN SEQRES 23 B 309 TYR GLY TYR PHE SER LYS GLN GLN GLN GLU TYR MET CYS SEQRES 24 B 309 TYR HIS ARG GLU ASN VAL PHE LYS LYS LEU SEQRES 1 C 11 DC DC DA DT DG 5CM DG DC DT DG DA SEQRES 1 D 11 DT DC DA DG DC DG DC DA DT DG DG SEQRES 1 E 11 DC DC DA DT DG 5CM DG DC DT DG DA SEQRES 1 F 11 DT DC DA DG DC DG DC DA DT DG DG HET 5CM C 6 20 HET 5CM E 6 20 HET CL A 401 1 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 B 401 5 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 404 5 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 5CM 2(C10 H16 N3 O7 P) FORMUL 7 CL CL 1- FORMUL 8 SO4 9(O4 S 2-) FORMUL 17 HOH *86(H2 O) HELIX 1 AA1 THR A 11 GLY A 18 1 8 HELIX 2 AA2 SER A 33 MET A 39 1 7 HELIX 3 AA3 THR A 40 VAL A 42 5 3 HELIX 4 AA4 PRO A 72 ALA A 80 5 9 HELIX 5 AA5 ARG A 101 ALA A 104 5 4 HELIX 6 AA6 HIS A 105 ARG A 110 1 6 HELIX 7 AA7 PRO A 111 LEU A 113 5 3 HELIX 8 AA8 PRO A 135 GLY A 147 1 13 HELIX 9 AA9 GLY A 147 PHE A 155 1 9 HELIX 10 AB1 PHE A 157 SER A 175 1 19 HELIX 11 AB2 ASP A 181 ARG A 193 1 13 HELIX 12 AB3 GLY A 196 GLU A 206 1 11 HELIX 13 AB4 LEU A 216 LEU A 220 5 5 HELIX 14 AB5 PRO A 227 SER A 231 5 5 HELIX 15 AB6 ALA A 246 LYS A 255 1 10 HELIX 16 AB7 LEU A 274 TRP A 280 1 7 HELIX 17 AB8 SER A 291 VAL A 305 1 15 HELIX 18 AB9 THR B 11 GLY B 18 1 8 HELIX 19 AC1 SER B 33 MET B 39 1 7 HELIX 20 AC2 THR B 40 VAL B 42 5 3 HELIX 21 AC3 PRO B 72 ALA B 80 5 9 HELIX 22 AC4 ARG B 101 ALA B 104 5 4 HELIX 23 AC5 HIS B 105 ARG B 110 1 6 HELIX 24 AC6 PRO B 111 LEU B 113 5 3 HELIX 25 AC7 PRO B 135 GLY B 147 1 13 HELIX 26 AC8 GLY B 147 PHE B 155 1 9 HELIX 27 AC9 PHE B 157 SER B 175 1 19 HELIX 28 AD1 ASP B 181 ARG B 193 1 13 HELIX 29 AD2 GLY B 196 GLU B 206 1 11 HELIX 30 AD3 LEU B 216 LEU B 220 5 5 HELIX 31 AD4 PRO B 227 SER B 231 5 5 HELIX 32 AD5 ASN B 232 LEU B 237 1 6 HELIX 33 AD6 ALA B 246 LYS B 255 1 10 HELIX 34 AD7 LEU B 274 TRP B 280 1 7 HELIX 35 AD8 SER B 291 VAL B 305 1 15 SHEET 1 AA1 3 TYR A 20 PRO A 24 0 SHEET 2 AA1 3 ASP A 85 GLU A 92 -1 O ILE A 89 N MET A 21 SHEET 3 AA1 3 TYR A 67 ASN A 70 -1 N TYR A 67 O LYS A 88 SHEET 1 AA2 6 TYR A 20 PRO A 24 0 SHEET 2 AA2 6 ASP A 85 GLU A 92 -1 O ILE A 89 N MET A 21 SHEET 3 AA2 6 LEU A 55 ALA A 62 -1 N ILE A 61 O GLU A 92 SHEET 4 AA2 6 VAL A 47 ALA A 52 -1 N VAL A 48 O GLY A 60 SHEET 5 AA2 6 TYR A 3 SER A 7 1 N TRP A 4 O PHE A 49 SHEET 6 AA2 6 LEU A 131 VAL A 134 -1 O PHE A 132 N TRP A 5 SHEET 1 AA3 2 ILE A 221 SER A 223 0 SHEET 2 AA3 2 LEU A 243 LEU A 245 -1 O LEU A 245 N ILE A 221 SHEET 1 AA4 2 ILE A 258 PHE A 260 0 SHEET 2 AA4 2 MET A 266 VAL A 268 -1 O ILE A 267 N SER A 259 SHEET 1 AA5 3 TYR B 20 PRO B 24 0 SHEET 2 AA5 3 ASP B 85 GLU B 92 -1 O ILE B 89 N MET B 21 SHEET 3 AA5 3 TYR B 67 ASN B 70 -1 N TYR B 67 O LYS B 88 SHEET 1 AA6 6 TYR B 20 PRO B 24 0 SHEET 2 AA6 6 ASP B 85 GLU B 92 -1 O ILE B 89 N MET B 21 SHEET 3 AA6 6 LEU B 55 ALA B 62 -1 N ILE B 61 O GLU B 92 SHEET 4 AA6 6 VAL B 47 ALA B 52 -1 N VAL B 48 O GLY B 60 SHEET 5 AA6 6 TYR B 3 SER B 7 1 N TRP B 4 O PHE B 49 SHEET 6 AA6 6 LEU B 131 VAL B 134 -1 O PHE B 132 N TRP B 5 SHEET 1 AA7 2 ILE B 221 SER B 223 0 SHEET 2 AA7 2 LEU B 243 LEU B 245 -1 O LEU B 245 N ILE B 221 SHEET 1 AA8 2 ILE B 258 PHE B 260 0 SHEET 2 AA8 2 MET B 266 VAL B 268 -1 O ILE B 267 N SER B 259 LINK O3' DG C 5 P 5CM C 6 1555 1555 1.58 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.61 LINK O3' DG E 5 P 5CM E 6 1555 1555 1.58 LINK O3' 5CM E 6 P DG E 7 1555 1555 1.60 SITE 1 AC1 2 LYS A 292 GLN A 293 SITE 1 AC2 2 SER A 64 HIS A 65 SITE 1 AC3 2 THR A 164 ARG A 192 SITE 1 AC4 3 ALA A 83 ASN A 84 ASP A 85 SITE 1 AC5 2 PRO A 135 HIS A 136 SITE 1 AC6 3 HIS A 34 ASN A 37 TYR A 117 SITE 1 AC7 2 SER B 64 HIS B 65 SITE 1 AC8 2 PRO B 135 HIS B 136 SITE 1 AC9 3 THR B 164 ALA B 167 ARG B 192 SITE 1 AD1 2 HIS B 34 ASN B 37 SITE 1 AD2 20 SER B 7 GLN B 8 LYS B 9 GLN B 10 SITE 2 AD2 20 THR B 11 GLU B 15 TRP B 22 ASN B 27 SITE 3 AD2 20 LYS B 28 TYR B 36 TRP B 82 GLN B 128 SITE 4 AD2 20 ALA B 129 TYR B 130 DT E 4 DG E 7 SITE 5 AD2 20 HOH E 101 DG F 6 DC F 7 DA F 8 SITE 1 AD3 19 SER B 7 GLN B 8 LYS B 9 GLN B 10 SITE 2 AD3 19 THR B 11 GLU B 15 TRP B 22 TYR B 36 SITE 3 AD3 19 TRP B 82 GLY B 126 ASN B 127 GLN B 128 SITE 4 AD3 19 ALA B 129 TYR B 130 DG E 5 DC E 8 SITE 5 AD3 19 DG F 4 DC F 5 DG F 6 CRYST1 81.111 81.111 617.307 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 0.012329 0.007118 0.000000 0.00000 SCALE2 0.000000 0.014236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001620 0.00000