HEADER HYDROLASE 23-SEP-17 6EJS TITLE NUCLEASE NUCB FROM BACILLUS LICHENIFORMIS IN P212121 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PUTATIVE EC 3.1.21.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 GENE: NUCB, BL00126; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1423 KEYWDS NUCLEASE, DNASE, METAL DEPENDENT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.STRANSKY,J.DOHNALEK,L.A.OESTERGAARD REVDAT 1 10-APR-19 6EJS 0 JRNL AUTH J.STRANSKY,J.DOHNALEK,L.H.OESTERGAARD JRNL TITL STRUCTURE OF NOVEL NUCLEASE NUCB FROM BACILLUS LICHENIFORMIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : CCP4 GEOMETRIC LIBRARY, VERSION 4.11 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 10766 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) : 0.188 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 492 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 661 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.2050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 838 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -0.17000 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 957 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 855 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1302 ; 1.778 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1979 ; 3.782 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 126 ; 5.786 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 47 ;34.778 ;21.064 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 160 ;14.653 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 130 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1106 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 229 ; 0.013 ; 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): 468 ; 1.337 ; 1.498 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 467 ; 1.304 ; 1.492 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 594 ; 1.947 ; 2.236 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6EJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-12 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.9,0.9184 REMARK 200 MONOCHROMATOR : 2 MIRROR AND DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.11600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULPHATE, 0.1 M TRIS PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 16.26700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.13100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.70700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.13100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.26700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.70700 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 A 33 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 92 O4 SO4 A 202 2.13 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6EJT RELATED DB: PDB REMARK 900 DIFFERENT CONDITION REMARK 900 RELATED ID: 6EJU RELATED DB: PDB REMARK 900 DIFFERENT CONDITION REMARK 900 RELATED ID: 6EJV RELATED DB: PDB REMARK 900 DIFFERENT CONDITION DBREF 6EJS A 33 142 UNP Q65J43 Q65J43_BACLD 33 142 SEQRES 1 A 110 ALA ALA ARG TYR ASP ASP ILE LEU TYR PHE PRO ALA SER SEQRES 2 A 110 ARG TYR PRO GLU THR GLY ALA HIS ILE SER ASP ALA ILE SEQRES 3 A 110 LYS ALA GLY HIS SER ASP VAL CYS THR ILE GLU ARG SER SEQRES 4 A 110 GLY ALA ASP LYS ARG ARG GLN GLU SER LEU LYS GLY ILE SEQRES 5 A 110 PRO THR LYS PRO GLY PHE ASP ARG ASP GLU TRP PRO MET SEQRES 6 A 110 ALA MET CYS GLU GLU GLY GLY LYS GLY ALA SER VAL ARG SEQRES 7 A 110 TYR VAL SER SER SER ASP ASN ARG GLY ALA GLY SER TRP SEQRES 8 A 110 VAL GLY ASN ARG LEU SER GLY PHE ALA ASP GLY THR ARG SEQRES 9 A 110 ILE LEU PHE ILE VAL GLN HET SO4 A 201 5 HET SO4 A 202 10 HET SO4 A 203 10 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *139(H2 O) HELIX 1 AA1 TYR A 47 GLY A 61 1 15 HELIX 2 AA2 GLY A 72 LEU A 81 1 10 HELIX 3 AA3 SER A 114 ARG A 118 1 5 HELIX 4 AA4 GLY A 119 LEU A 128 1 10 SHEET 1 AA1 3 ASP A 38 PHE A 42 0 SHEET 2 AA1 3 ARG A 136 VAL A 141 1 O LEU A 138 N LEU A 40 SHEET 3 AA1 3 VAL A 65 THR A 67 -1 N CYS A 66 O ILE A 137 SHEET 1 AA2 2 PHE A 90 TRP A 95 0 SHEET 2 AA2 2 SER A 108 SER A 113 -1 O SER A 108 N TRP A 95 SSBOND 1 CYS A 66 CYS A 100 1555 1555 2.07 CISPEP 1 TRP A 95 PRO A 96 0 -1.79 SITE 1 AC1 7 ARG A 118 GLY A 119 ALA A 120 GLY A 121 SITE 2 AC1 7 SER A 122 HOH A 301 HOH A 315 SITE 1 AC2 9 ALA A 34 ARG A 35 TYR A 36 ARG A 77 SITE 2 AC2 9 ASP A 91 ARG A 92 HOH A 306 HOH A 310 SITE 3 AC2 9 HOH A 353 SITE 1 AC3 12 ARG A 35 ARG A 46 ARG A 77 TRP A 123 SITE 2 AC3 12 ARG A 127 ARG A 136 HOH A 305 HOH A 322 SITE 3 AC3 12 HOH A 342 HOH A 368 HOH A 388 HOH A 391 CRYST1 32.534 47.414 56.262 90.00 90.00 90.00 P 21 21 21 4 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 0.030737 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017774 0.00000