HEADER HYDROLASE 25-MAR-20 6YEX TITLE VCAM4I RESTRICTION ENDONUCLEASE IN THE ABSENCE OF DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNH ENDONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 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) KEYWDS PUA SUPERFAMILY, EVE DOMAIN, DNA ENDONUCLEASE, MODIFICATION-DEPENDENT KEYWDS 2 RESTRICTION ENDONUCLEASE, MDRE, SINGLE STRANDED DNA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PASTOR,H.CZAPINSKA,T.LUTZ,I.HELBRECHT,S.XU,M.BOCHTLER REVDAT 5 15-MAY-24 6YEX 1 REMARK REVDAT 4 03-MAR-21 6YEX 1 JRNL REVDAT 3 27-JAN-21 6YEX 1 JRNL REVDAT 2 23-DEC-20 6YEX 1 JRNL REVDAT 1 16-DEC-20 6YEX 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 105907 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 15090 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 283 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 1024 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.14000 REMARK 3 B22 (A**2) : 2.66000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.00000 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.305 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5641 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4936 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7698 ; 1.131 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11569 ; 0.726 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 714 ; 5.837 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;36.035 ;24.950 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 989 ;12.025 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;19.725 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 782 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6588 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1195 ; 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 : 4 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 157 A 309 REMARK 3 RESIDUE RANGE : B 182 B 309 REMARK 3 RESIDUE RANGE : C 1 C 2000 REMARK 3 RESIDUE RANGE : D 1 D 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5542 30.5286 28.8684 REMARK 3 T TENSOR REMARK 3 T11: 0.1370 T22: 0.0341 REMARK 3 T33: 0.1269 T12: -0.0165 REMARK 3 T13: 0.0334 T23: -0.0572 REMARK 3 L TENSOR REMARK 3 L11: 0.8231 L22: 0.3046 REMARK 3 L33: 0.4844 L12: 0.0284 REMARK 3 L13: 0.0904 L23: -0.2338 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: 0.0385 S13: -0.0500 REMARK 3 S21: 0.0544 S22: -0.0679 S23: 0.0483 REMARK 3 S31: -0.0253 S32: 0.0072 S33: 0.0818 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 1 A 156 REMARK 3 RESIDUE RANGE : E 1 E 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 36.7723 19.1223 51.4107 REMARK 3 T TENSOR REMARK 3 T11: 0.1907 T22: 0.0424 REMARK 3 T33: 0.0808 T12: -0.0551 REMARK 3 T13: 0.0124 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.0070 L22: 1.2118 REMARK 3 L33: 0.6106 L12: -0.4761 REMARK 3 L13: 0.0572 L23: -0.2333 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: -0.1580 S13: -0.0411 REMARK 3 S21: 0.2282 S22: -0.0071 S23: -0.0041 REMARK 3 S31: -0.0761 S32: 0.0460 S33: 0.0005 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 156 REMARK 3 RESIDUE RANGE : F 1 F 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0594 27.2833 -1.5962 REMARK 3 T TENSOR REMARK 3 T11: 0.0349 T22: 0.3626 REMARK 3 T33: 0.1265 T12: 0.0237 REMARK 3 T13: -0.0403 T23: -0.1855 REMARK 3 L TENSOR REMARK 3 L11: 0.3520 L22: 1.9746 REMARK 3 L33: 2.3580 L12: -0.4967 REMARK 3 L13: -0.8009 L23: 0.9467 REMARK 3 S TENSOR REMARK 3 S11: 0.0555 S12: 0.2628 S13: -0.1629 REMARK 3 S21: -0.1130 S22: -0.3795 S23: 0.1703 REMARK 3 S31: -0.1901 S32: -0.3320 S33: 0.3240 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 157 B 181 REMARK 3 RESIDUE RANGE : G 1 G 2000 REMARK 3 ORIGIN FOR THE GROUP (A): 33.3228 24.9712 18.5595 REMARK 3 T TENSOR REMARK 3 T11: 0.1059 T22: 0.1533 REMARK 3 T33: 0.1102 T12: 0.0764 REMARK 3 T13: -0.0425 T23: -0.1195 REMARK 3 L TENSOR REMARK 3 L11: 7.9945 L22: 2.2048 REMARK 3 L33: 2.9454 L12: -3.4541 REMARK 3 L13: 4.2823 L23: -2.5314 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: 0.3072 S13: 0.0190 REMARK 3 S21: -0.1345 S22: -0.1179 S23: -0.0847 REMARK 3 S31: 0.1315 S32: 0.1470 S33: 0.0880 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 U VALUES : WITH TLS ADDED REMARK 3 THE IDENTITY OF THE SOLVENT MOLECULES HAS BEEN ASSIGNED REMARK 3 TENTATIVELY. REMARK 4 REMARK 4 6YEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292105842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0064 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 : 107966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 26.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.06200 REMARK 200 FOR SHELL : 2.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (7.2 MG/ML) IN 0.27 M NACL, REMARK 280 13.5 MM TRIS-HCL PH 8.5, 0.2 M SODIUM MALONATE AND 0.9 MM TCEP REMARK 280 WAS MIXED IN 1:1 RATIO WITH RESERVOIR SOLUTION (1.8 M AMMONIUM REMARK 280 SULFATE, 0.1 M MES PH 5.25). PERFLUOROPOLYETHER OIL WAS USED AS REMARK 280 A CRYOPROTECTANT., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 28.48500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.13050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.76600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.13050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.48500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.76600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE MODIFICATION SPECIFIC VCAM4I RESTRICTION ENDONUCLEASE REMARK 300 IS ACTIVE AS A DIMER (EACH PROTOMER CLEAVES ONE STRAND OF THE REMARK 300 DOUBLE STRANDED DNA SUBSTRATE). THE C-TERMINAL HNH NUCLEASE DOMAINS REMARK 300 MEDIATE THE DIMERIZATION. THE N-TERMINAL EVE DOMAINS ARE REMARK 300 RESPONSIBLE FOR THE MODIFICATION SPECIFICITY. 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: 6830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -183.0 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 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 ALA B 78 REMARK 465 GLY B 79 REMARK 465 ALA B 80 REMARK 465 ASP B 81 REMARK 465 TRP B 82 REMARK 465 ALA B 83 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 LYS A 9 -107.65 55.74 REMARK 500 LYS A 9 -106.97 55.74 REMARK 500 ALA A 78 105.16 -49.24 REMARK 500 TYR A 130 -64.13 -99.53 REMARK 500 PHE A 157 -88.14 -140.44 REMARK 500 ILE A 225 -66.73 -95.50 REMARK 500 ASN A 241 53.60 -96.82 REMARK 500 LYS B 9 -106.61 56.68 REMARK 500 TYR B 130 -60.24 -96.67 REMARK 500 PHE B 157 -89.70 -135.81 REMARK 500 ILE B 225 -66.34 -92.19 REMARK 500 ASN B 241 52.60 -100.79 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 A1022 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1023 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1024 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A1025 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A1026 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A1027 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A1028 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A1029 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH B 993 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B 994 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH B 995 DISTANCE = 6.38 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 CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 412 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: 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 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 6YEX A 1 309 UNP A0A344KQF3_9VIBR DBREF2 6YEX A A0A344KQF3 1 309 DBREF1 6YEX B 1 309 UNP A0A344KQF3_9VIBR DBREF2 6YEX B A0A344KQF3 1 309 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 HET SO4 A 401 5 HET SO4 A 402 5 HET CL A 403 1 HET CL A 404 1 HET CL A 405 1 HET CL A 406 1 HET CL A 407 1 HET SO4 B 401 5 HET CL B 402 1 HET CL B 403 1 HET SO4 B 404 5 HET SO4 B 405 5 HET SO4 B 406 5 HET SO4 B 407 5 HET CL B 408 1 HET CL B 409 1 HET CL B 410 1 HET CL B 411 1 HET CL B 412 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 3 SO4 7(O4 S 2-) FORMUL 5 CL 12(CL 1-) FORMUL 22 HOH *1024(H2 O) HELIX 1 AA1 THR A 11 GLY A 19 1 9 HELIX 2 AA2 SER A 33 THR A 40 1 8 HELIX 3 AA3 ALA A 80 ALA A 83 5 4 HELIX 4 AA4 ARG A 101 ALA A 104 5 4 HELIX 5 AA5 HIS A 105 ARG A 110 1 6 HELIX 6 AA6 PRO A 111 LEU A 113 5 3 HELIX 7 AA7 PRO A 135 GLY A 147 1 13 HELIX 8 AA8 GLY A 147 PHE A 155 1 9 HELIX 9 AA9 PHE A 157 ASP A 159 5 3 HELIX 10 AB1 THR A 160 ASN A 176 1 17 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 ASN A 232 LEU A 237 1 6 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 19 1 9 HELIX 19 AC1 SER B 33 ASN B 38 1 6 HELIX 20 AC2 MET B 39 VAL B 42 5 4 HELIX 21 AC3 ARG B 101 ALA B 104 5 4 HELIX 22 AC4 HIS B 105 ARG B 110 1 6 HELIX 23 AC5 PRO B 111 LEU B 113 5 3 HELIX 24 AC6 PRO B 135 GLY B 147 1 13 HELIX 25 AC7 GLY B 147 PHE B 155 1 9 HELIX 26 AC8 PHE B 157 ASP B 159 5 3 HELIX 27 AC9 THR B 160 ASN B 176 1 17 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 ASN B 232 LEU B 237 1 6 HELIX 32 AD5 ALA B 246 LYS B 255 1 10 HELIX 33 AD6 ASN B 273 TRP B 280 1 8 HELIX 34 AD7 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 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 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 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 SHEET 1 AA5 3 TYR B 20 SER B 23 0 SHEET 2 AA5 3 GLY B 86 GLU B 92 -1 O TRP B 87 N SER B 23 SHEET 3 AA5 3 TYR B 67 TYR B 69 -1 N TYR B 69 O GLY B 86 SHEET 1 AA6 6 TYR B 20 SER B 23 0 SHEET 2 AA6 6 GLY B 86 GLU B 92 -1 O TRP B 87 N SER B 23 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 ALA B 52 O LEU B 55 SHEET 5 AA6 6 TYR B 3 SER B 7 1 N VAL B 6 O PHE B 51 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 HIS B 224 0 SHEET 2 AA7 2 GLY B 242 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 SITE 1 AC1 8 SER A 64 HIS A 65 HOH A 509 HOH A 518 SITE 2 AC1 8 HOH A 559 HOH A 719 HOH A 723 HOH B 542 SITE 1 AC2 4 PRO A 135 HIS A 136 HOH A 631 HOH A 653 SITE 1 AC3 2 HIS A 34 HOH B 935 SITE 1 AC4 1 ASP A 122 SITE 1 AC5 1 TYR A 117 SITE 1 AC6 1 SER A 68 SITE 1 AC7 1 GLY A 126 SITE 1 AC8 7 SER B 291 LYS B 292 GLN B 293 HOH B 515 SITE 2 AC8 7 HOH B 546 HOH B 586 HOH B 693 SITE 1 AC9 6 HOH A 574 GLU B 261 ASP B 262 ARG B 302 SITE 2 AC9 6 HOH B 843 HOH B 876 SITE 1 AD1 3 ASP B 238 GLY B 239 HOH B 900 SITE 1 AD2 5 ASN A 29 HOH A1007 GLY B 147 SER B 148 SITE 2 AD2 5 HOH B 606 SITE 1 AD3 7 HOH A 669 ASN B 27 SER B 33 HIS B 34 SITE 2 AD3 7 TYR B 35 HOH B 519 HOH B 644 SITE 1 AD4 8 SER B 64 HIS B 65 HOH B 506 HOH B 524 SITE 2 AD4 8 HOH B 605 HOH B 618 HOH B 672 HOH B 786 SITE 1 AD5 3 PRO B 135 HIS B 136 HOH B 735 SITE 1 AD6 3 TYR B 67 SER B 68 ARG B 101 SITE 1 AD7 4 ILE B 100 ARG B 101 HIS B 105 HOH B 825 SITE 1 AD8 4 HOH A 513 HOH A 685 THR B 31 GLN B 32 SITE 1 AD9 4 HIS B 34 ASN B 38 TYR B 117 SER B 133 SITE 1 AE1 3 ASN B 37 HOH B 892 HOH B 970 CRYST1 56.970 93.532 126.261 90.00 90.00 90.00 P 21 21 21 8 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 0.017553 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007920 0.00000