HEADER HYDROLASE 06-APR-20 6YKF TITLE VCAM4I RESTRICTION ENDONUCLEASE IN THE PRESENCE OF 5MC-MODIFIED SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNH ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*(5CM)P*AP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 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 KEYWDS PUA SUPERFAMILY, EVE DOMAIN, DNA ENDONUCLEASE, MODIFICATION-DEPENDENT KEYWDS 2 RESTRICTION ENDONUCLEASE, MDRE, 5-HYDROXYMETHYLCYTOSINE, 5- KEYWDS 3 METHYLCYTOSINE, SINGLE STRANDED DNA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PASTOR,H.CZAPINSKA,T.LUTZ,I.HELBRECHT,S.XU,M.BOCHTLER REVDAT 4 24-JAN-24 6YKF 1 REMARK REVDAT 3 03-MAR-21 6YKF 1 JRNL REVDAT 2 27-JAN-21 6YKF 1 JRNL REVDAT 1 23-DEC-20 6YKF 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. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 85724 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4481 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE SET COUNT : 327 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2499 REMARK 3 NUCLEIC ACID ATOMS : 100 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 586 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72000 REMARK 3 B22 (A**2) : 0.72000 REMARK 3 B33 (A**2) : -2.34000 REMARK 3 B12 (A**2) : 0.36000 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): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.674 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3160 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2742 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4329 ; 1.288 ; 1.626 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6440 ; 1.384 ; 1.613 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 6.436 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;34.110 ;23.772 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;13.630 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.085 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3590 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 672 ; 0.002 ; 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 : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 181 REMARK 3 RESIDUE RANGE : B 1 B 5 REMARK 3 RESIDUE RANGE : C 1 C 2000 REMARK 3 RESIDUE RANGE : D 1 D 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5580 -56.7997 -19.4123 REMARK 3 T TENSOR REMARK 3 T11: 0.0268 T22: 0.0466 REMARK 3 T33: 0.1718 T12: -0.0092 REMARK 3 T13: 0.0053 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.6175 L22: 0.0220 REMARK 3 L33: 0.3832 L12: 0.0968 REMARK 3 L13: 0.0122 L23: -0.0389 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: 0.0005 S13: 0.0727 REMARK 3 S21: -0.0002 S22: -0.0040 S23: 0.0292 REMARK 3 S31: -0.0201 S32: 0.0285 S33: -0.0026 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 182 A 310 REMARK 3 RESIDUE RANGE : E 1 E 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 34.3401 -43.1612 -6.3165 REMARK 3 T TENSOR REMARK 3 T11: 0.0117 T22: 0.1134 REMARK 3 T33: 0.1924 T12: -0.0165 REMARK 3 T13: 0.0149 T23: -0.0335 REMARK 3 L TENSOR REMARK 3 L11: 1.4568 L22: 0.1504 REMARK 3 L33: 0.3199 L12: 0.1502 REMARK 3 L13: -0.2925 L23: 0.0719 REMARK 3 S TENSOR REMARK 3 S11: 0.1167 S12: -0.1061 S13: 0.2109 REMARK 3 S21: 0.0244 S22: -0.1286 S23: 0.0146 REMARK 3 S31: -0.0097 S32: -0.0330 S33: 0.0120 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 CONFORMATION OF TWO REMARK 3 RESIDUES AT THE 5' END OF THE OLIGONUCLEOTIDE IS UNCERTAIN THE REMARK 3 IDENTITY OF THE SOLVENT MOLECULES HAS BEEN ASSIGNED TENTATIVELY. REMARK 4 REMARK 4 6YKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292106329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-19 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90208 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 42.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09100 REMARK 200 FOR THE DATA SET : 14.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.96700 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: REFMAC REMARK 200 STARTING MODEL: 6YJB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 1.6 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 62 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 73.94067 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 36.97033 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 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 73.94067 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 36.97033 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 73.94067 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 36.97033 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 73.94067 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 0.00000 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 36.97033 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O2 GOL A 410 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 618 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 718 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 919 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 PHE A 157 -91.78 -135.14 REMARK 500 ASN A 241 52.05 -98.98 REMARK 500 ASN A 304 -31.22 -131.81 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 A1056 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A1057 DISTANCE = 6.90 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 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 GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 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: 6YMG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VCAM4I RESTRICTION ENDONUCLEASE IN THE REMARK 900 PRESENCE OF 5MC-MODIFIED DSDNA DBREF1 6YKF A 1 309 UNP A0A344KQF3_9VIBR DBREF2 6YKF A A0A344KQF3 1 309 DBREF 6YKF B 1 5 PDB 6YKF 6YKF 1 5 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 5 DC DA 5CM DA DG HET 5CM B 3 20 HET SO4 A 401 5 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 GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HET GOL A 410 6 HET GOL A 411 6 HET GOL A 412 6 HET GOL A 413 6 HET GOL A 414 6 HET CL A 415 1 HET GOL A 416 6 HET SO4 A 417 10 HET SO4 A 418 5 HET SO4 A 419 5 HET SO4 A 420 5 HET GOL B 101 6 HET SO4 B 102 5 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 3 SO4 11(O4 S 2-) FORMUL 9 GOL 10(C3 H8 O3) FORMUL 17 CL CL 1- FORMUL 25 HOH *586(H2 O) HELIX 1 AA1 THR A 11 GLY A 19 1 9 HELIX 2 AA2 SER A 33 ASN A 38 1 6 HELIX 3 AA3 MET A 39 VAL A 42 5 4 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 ASP A 159 5 3 HELIX 11 AB2 THR A 160 ASN A 176 1 17 HELIX 12 AB3 ASP A 181 ARG A 192 1 12 HELIX 13 AB4 ARG A 193 GLN A 195 5 3 HELIX 14 AB5 GLY A 196 GLU A 206 1 11 HELIX 15 AB6 LEU A 216 LEU A 220 5 5 HELIX 16 AB7 ASN A 232 LEU A 237 1 6 HELIX 17 AB8 ALA A 246 LYS A 255 1 10 HELIX 18 AB9 ASN A 273 TRP A 280 1 8 HELIX 19 AC1 SER A 291 VAL A 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 TRP A 87 N SER A 23 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 TRP A 87 N SER A 23 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 VAL A 6 O PHE A 51 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 HIS A 224 0 SHEET 2 AA3 2 GLY A 242 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 LINK O3' DA B 2 P 5CM B 3 1555 1555 1.59 LINK O3' 5CM B 3 P DA B 4 1555 1555 1.59 SITE 1 AC1 7 SER A 64 HIS A 65 HOH A 513 HOH A 516 SITE 2 AC1 7 HOH A 555 HOH A 851 HOH A 892 SITE 1 AC2 5 PRO A 135 HIS A 136 HOH A 521 HOH A 601 SITE 2 AC2 5 HOH A 712 SITE 1 AC3 10 ASN A 27 GLN A 32 SER A 33 HIS A 34 SITE 2 AC3 10 TYR A 35 HOH A 510 HOH A 998 DC B 1 SITE 3 AC3 10 HOH B 201 HOH B 225 SITE 1 AC4 7 HIS A 34 ASN A 37 LYS A 292 HOH A 587 SITE 2 AC4 7 HOH A 818 HOH A 949 HOH A 991 SITE 1 AC5 8 LYS A 25 ALA A 178 SER A 179 ILE A 180 SITE 2 AC5 8 ASP A 181 GOL A 409 HOH A 827 HOH A 836 SITE 1 AC6 12 LYS A 28 ASN A 70 THR A 73 ALA A 83 SITE 2 AC6 12 ASN A 84 ASP A 85 HOH A 527 HOH A 557 SITE 3 AC6 12 HOH A 708 HOH A 860 HOH A1034 HOH A1048 SITE 1 AC7 16 ALA A 78 GLY A 79 ALA A 80 ASP A 81 SITE 2 AC7 16 TRP A 82 HOH A 506 HOH A 520 HOH A 545 SITE 3 AC7 16 HOH A 662 HOH A 726 HOH A 871 HOH A1011 SITE 4 AC7 16 5CM B 3 GOL B 101 HOH B 204 HOH B 207 SITE 1 AC8 11 PHE A 16 GLU A 17 ILE A 197 SER A 200 SITE 2 AC8 11 ARG A 201 GLN A 204 HOH A 598 HOH A 616 SITE 3 AC8 11 HOH A1017 HOH A1023 HOH A1035 SITE 1 AC9 13 SER A 68 TYR A 69 ASN A 70 ASP A 85 SITE 2 AC9 13 ASP A 181 SO4 A 405 HOH A 551 HOH A 669 SITE 3 AC9 13 HOH A 717 HOH A 749 HOH A 789 HOH A 990 SITE 4 AC9 13 HOH A 992 SITE 1 AD1 9 LYS A 9 GLN A 10 ASN A 53 ALA A 78 SITE 2 AD1 9 GOL A 411 HOH A 507 HOH A 535 HOH A 750 SITE 3 AD1 9 HOH A 919 SITE 1 AD2 8 GLN A 10 PHE A 12 LYS A 13 GLN A 14 SITE 2 AD2 8 GOL A 410 HOH A 509 HOH A 524 HOH A 750 SITE 1 AD3 10 LYS A 103 ALA A 104 ILE A 106 SER A 148 SITE 2 AD3 10 ASN A 273 HOH A 599 HOH A 642 HOH A 654 SITE 3 AD3 10 HOH A 943 HOH A1056 SITE 1 AD4 10 ASP A 107 SER A 148 GLU A 151 ASN A 218 SITE 2 AD4 10 LYS A 271 HOH A 502 HOH A 573 HOH A 705 SITE 3 AD4 10 HOH A 862 HOH A 978 SITE 1 AD5 10 LEU A 55 GLU A 97 LYS A 99 ARG A 101 SITE 2 AD5 10 HOH A 512 HOH A 577 HOH A 618 HOH A 638 SITE 3 AD5 10 HOH A 824 HOH A 882 SITE 1 AD6 3 TYR A 67 SER A 68 HOH A 748 SITE 1 AD7 11 GLY A 156 PHE A 157 THR A 160 ARG A 199 SITE 2 AD7 11 LYS A 217 ASN A 218 LEU A 220 LYS A 255 SITE 3 AD7 11 HOH A 519 HOH A 604 HOH A 853 SITE 1 AD8 8 THR A 31 GLN A 32 SER A 291 LYS A 292 SITE 2 AD8 8 GLN A 293 HOH A 653 HOH A 685 HOH A 764 SITE 1 AD9 4 ASN A 232 ASN A 233 HOH A 503 HOH A 670 SITE 1 AE1 5 ARG A 201 LEU A 237 HOH A 546 HOH A 585 SITE 2 AE1 5 HOH A 609 SITE 1 AE2 6 THR A 164 ALA A 167 ARG A 192 HOH A 614 SITE 2 AE2 6 HOH A 886 HOH A 890 SITE 1 AE3 13 LYS A 9 GLN A 10 GLN A 128 GOL A 407 SITE 2 AE3 13 HOH A 506 HOH A 520 HOH A 847 HOH A 873 SITE 3 AE3 13 5CM B 3 DA B 4 DG B 5 SO4 B 102 SITE 4 AE3 13 HOH B 207 SITE 1 AE4 9 LYS A 9 DA B 4 DG B 5 GOL B 101 SITE 2 AE4 9 HOH B 209 HOH B 215 HOH B 219 HOH B 223 SITE 3 AE4 9 HOH B 224 CRYST1 129.000 129.000 110.911 90.00 90.00 120.00 P 62 2 2 12 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 0.007752 0.004476 0.000000 0.00000 SCALE2 0.000000 0.008951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009016 0.00000