HEADER HYDROLASE 08-MAY-09 3HEJ TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS T62R AT TITLE 2 CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A, D, B, C; COMPND 4 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE, COMPND 5 NUCLEASE B, NUCLEASE A; COMPND 6 EC: 3.1.31.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: NUC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS STAPHYLOCOCCAL NUCLEASE, HYPERSTABLE VARIANT, HYDROLASE, PDTP, DOMAIN KEYWDS 2 SWAPPING, ARGININE, CALCIUM, ENDONUCLEASE, MEMBRANE, METAL-BINDING, KEYWDS 3 NUCLEASE, SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR V.S.KHANGULOV,J.L.SCHLESSMAN,A.HEROUX,E.B.GARCIA-MORENO REVDAT 4 21-FEB-24 3HEJ 1 REMARK REVDAT 3 13-OCT-21 3HEJ 1 REMARK SEQADV REVDAT 2 01-NOV-17 3HEJ 1 REMARK REVDAT 1 19-MAY-10 3HEJ 0 JRNL AUTH V.S.KHANGULOV,J.L.SCHLESSMAN,A.HEROUX,E.B.GARCIA-MORENO JRNL TITL DOMAIN SWAPPING PROMOTED BY A SINGLE MUTATION THAT JRNL TITL 2 INTRODUCES AN IONIZABLE GROUP INTO THE HYDROPHOBIC CORE OF A JRNL TITL 3 PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 62385 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3162 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4289 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.4290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4320 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 478 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.36000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : -0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.42000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.851 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4662 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6293 ; 1.239 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 577 ; 5.807 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;34.287 ;24.581 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 928 ;15.359 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;16.020 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 676 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3374 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2739 ; 1.787 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4407 ; 2.763 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1923 ; 4.594 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1865 ; 6.585 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3HEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MERIDIONALLY-BENT FUSED SILICA REMARK 200 MIRROR WITH PALLADIUM AND REMARK 200 UNCOATED STRIPES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 68.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, 5% GLYCEROL, PDTP, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.21000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 GLU A 142 REMARK 465 ASP A 143 REMARK 465 ASN A 144 REMARK 465 ALA A 145 REMARK 465 ASP A 146 REMARK 465 SER A 147 REMARK 465 GLY A 148 REMARK 465 GLN A 149 REMARK 465 GLU D 142 REMARK 465 ASP D 143 REMARK 465 ASN D 144 REMARK 465 ALA D 145 REMARK 465 ASP D 146 REMARK 465 SER D 147 REMARK 465 GLY D 148 REMARK 465 GLN D 149 REMARK 465 GLU B 142 REMARK 465 ASP B 143 REMARK 465 ASN B 144 REMARK 465 ALA B 145 REMARK 465 ASP B 146 REMARK 465 SER B 147 REMARK 465 GLY B 148 REMARK 465 GLN B 149 REMARK 465 GLU C 142 REMARK 465 ASP C 143 REMARK 465 ASN C 144 REMARK 465 ALA C 145 REMARK 465 ASP C 146 REMARK 465 SER C 147 REMARK 465 GLY C 148 REMARK 465 GLN C 149 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 2 -36.18 -130.32 REMARK 500 LYS A 6 -123.43 -108.71 REMARK 500 TYR A 54 -5.67 72.15 REMARK 500 ASN A 138 -110.59 50.29 REMARK 500 TYR D 54 -9.78 76.60 REMARK 500 ASP D 95 52.51 36.20 REMARK 500 ASN D 138 -107.21 50.84 REMARK 500 LYS B 6 -121.72 -107.67 REMARK 500 TYR B 54 -2.24 71.63 REMARK 500 ASN B 138 -107.69 50.56 REMARK 500 TYR C 54 -7.68 68.66 REMARK 500 ASP C 95 52.32 39.59 REMARK 500 LYS C 116 127.44 -33.81 REMARK 500 ASN C 138 -105.22 53.68 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 THP A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP B 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP C 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP D 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD B 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 152 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS AT REMARK 900 CRYOGENIC TEMPERATURES REMARK 900 RELATED ID: 3HEH RELATED DB: PDB DBREF 3HEJ A 1 149 UNP P00644 NUC_STAAU 83 231 DBREF 3HEJ D 1 149 UNP P00644 NUC_STAAU 83 231 DBREF 3HEJ B 1 149 UNP P00644 NUC_STAAU 83 231 DBREF 3HEJ C 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3HEJ A UNP P00644 THR 126 DELETION SEQADV 3HEJ A UNP P00644 LYS 127 DELETION SEQADV 3HEJ A UNP P00644 HIS 128 DELETION SEQADV 3HEJ A UNP P00644 PRO 129 DELETION SEQADV 3HEJ A UNP P00644 LYS 130 DELETION SEQADV 3HEJ A UNP P00644 LYS 131 DELETION SEQADV 3HEJ PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3HEJ ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3HEJ ARG A 62 UNP P00644 THR 144 ENGINEERED MUTATION SEQADV 3HEJ GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3HEJ LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3HEJ ALA A 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQADV 3HEJ D UNP P00644 THR 126 DELETION SEQADV 3HEJ D UNP P00644 LYS 127 DELETION SEQADV 3HEJ D UNP P00644 HIS 128 DELETION SEQADV 3HEJ D UNP P00644 PRO 129 DELETION SEQADV 3HEJ D UNP P00644 LYS 130 DELETION SEQADV 3HEJ D UNP P00644 LYS 131 DELETION SEQADV 3HEJ PHE D 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3HEJ ASN D 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3HEJ ARG D 62 UNP P00644 THR 144 ENGINEERED MUTATION SEQADV 3HEJ GLY D 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3HEJ LEU D 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3HEJ ALA D 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQADV 3HEJ B UNP P00644 THR 126 DELETION SEQADV 3HEJ B UNP P00644 LYS 127 DELETION SEQADV 3HEJ B UNP P00644 HIS 128 DELETION SEQADV 3HEJ B UNP P00644 PRO 129 DELETION SEQADV 3HEJ B UNP P00644 LYS 130 DELETION SEQADV 3HEJ B UNP P00644 LYS 131 DELETION SEQADV 3HEJ PHE B 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3HEJ ASN B 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3HEJ ARG B 62 UNP P00644 THR 144 ENGINEERED MUTATION SEQADV 3HEJ GLY B 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3HEJ LEU B 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3HEJ ALA B 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQADV 3HEJ C UNP P00644 THR 126 DELETION SEQADV 3HEJ C UNP P00644 LYS 127 DELETION SEQADV 3HEJ C UNP P00644 HIS 128 DELETION SEQADV 3HEJ C UNP P00644 PRO 129 DELETION SEQADV 3HEJ C UNP P00644 LYS 130 DELETION SEQADV 3HEJ C UNP P00644 LYS 131 DELETION SEQADV 3HEJ PHE C 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3HEJ ASN C 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3HEJ ARG C 62 UNP P00644 THR 144 ENGINEERED MUTATION SEQADV 3HEJ GLY C 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3HEJ LEU C 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3HEJ ALA C 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQRES 1 A 143 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 A 143 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 A 143 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 143 ASP THR PRO GLU PHE ASN GLU LYS TYR GLY PRO GLU ALA SEQRES 5 A 143 SER ALA PHE ARG LYS LYS MET VAL GLU ASN ALA LYS LYS SEQRES 6 A 143 ILE GLU VAL GLU PHE ASP LYS GLY GLN ARG THR ASP LYS SEQRES 7 A 143 TYR GLY ARG GLY LEU ALA TYR ILE TYR ALA ASP GLY LYS SEQRES 8 A 143 MET VAL ASN GLU ALA LEU VAL ARG GLN GLY LEU ALA LYS SEQRES 9 A 143 VAL ALA TYR VAL TYR LYS GLY ASN ASN THR HIS GLU GLN SEQRES 10 A 143 LEU LEU ARG LYS ALA GLU ALA GLN ALA LYS LYS GLU LYS SEQRES 11 A 143 LEU ASN ILE TRP SER GLU ASP ASN ALA ASP SER GLY GLN SEQRES 1 D 143 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 D 143 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 D 143 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 D 143 ASP THR PRO GLU PHE ASN GLU LYS TYR GLY PRO GLU ALA SEQRES 5 D 143 SER ALA PHE ARG LYS LYS MET VAL GLU ASN ALA LYS LYS SEQRES 6 D 143 ILE GLU VAL GLU PHE ASP LYS GLY GLN ARG THR ASP LYS SEQRES 7 D 143 TYR GLY ARG GLY LEU ALA TYR ILE TYR ALA ASP GLY LYS SEQRES 8 D 143 MET VAL ASN GLU ALA LEU VAL ARG GLN GLY LEU ALA LYS SEQRES 9 D 143 VAL ALA TYR VAL TYR LYS GLY ASN ASN THR HIS GLU GLN SEQRES 10 D 143 LEU LEU ARG LYS ALA GLU ALA GLN ALA LYS LYS GLU LYS SEQRES 11 D 143 LEU ASN ILE TRP SER GLU ASP ASN ALA ASP SER GLY GLN SEQRES 1 B 143 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 B 143 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 B 143 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 B 143 ASP THR PRO GLU PHE ASN GLU LYS TYR GLY PRO GLU ALA SEQRES 5 B 143 SER ALA PHE ARG LYS LYS MET VAL GLU ASN ALA LYS LYS SEQRES 6 B 143 ILE GLU VAL GLU PHE ASP LYS GLY GLN ARG THR ASP LYS SEQRES 7 B 143 TYR GLY ARG GLY LEU ALA TYR ILE TYR ALA ASP GLY LYS SEQRES 8 B 143 MET VAL ASN GLU ALA LEU VAL ARG GLN GLY LEU ALA LYS SEQRES 9 B 143 VAL ALA TYR VAL TYR LYS GLY ASN ASN THR HIS GLU GLN SEQRES 10 B 143 LEU LEU ARG LYS ALA GLU ALA GLN ALA LYS LYS GLU LYS SEQRES 11 B 143 LEU ASN ILE TRP SER GLU ASP ASN ALA ASP SER GLY GLN SEQRES 1 C 143 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 C 143 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 C 143 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 C 143 ASP THR PRO GLU PHE ASN GLU LYS TYR GLY PRO GLU ALA SEQRES 5 C 143 SER ALA PHE ARG LYS LYS MET VAL GLU ASN ALA LYS LYS SEQRES 6 C 143 ILE GLU VAL GLU PHE ASP LYS GLY GLN ARG THR ASP LYS SEQRES 7 C 143 TYR GLY ARG GLY LEU ALA TYR ILE TYR ALA ASP GLY LYS SEQRES 8 C 143 MET VAL ASN GLU ALA LEU VAL ARG GLN GLY LEU ALA LYS SEQRES 9 C 143 VAL ALA TYR VAL TYR LYS GLY ASN ASN THR HIS GLU GLN SEQRES 10 C 143 LEU LEU ARG LYS ALA GLU ALA GLN ALA LYS LYS GLU LYS SEQRES 11 C 143 LEU ASN ILE TRP SER GLU ASP ASN ALA ASP SER GLY GLN HET THP A 150 25 HET MPD A 151 8 HET GOL A 152 6 HET THP D 150 25 HET THP B 150 25 HET MRD B 151 8 HET THP C 150 25 HET GOL C 151 6 HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM GOL GLYCEROL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 THP 4(C10 H16 N2 O11 P2) FORMUL 6 MPD C6 H14 O2 FORMUL 7 GOL 2(C3 H8 O3) FORMUL 10 MRD C6 H14 O2 FORMUL 13 HOH *478(H2 O) HELIX 1 1 TYR A 54 ASN A 68 1 15 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 GLU A 135 1 15 HELIX 4 4 LEU A 137 SER A 141 5 5 HELIX 5 5 TYR D 54 ASN D 68 1 15 HELIX 6 6 VAL D 99 GLN D 106 1 8 HELIX 7 7 HIS D 121 GLU D 135 1 15 HELIX 8 8 LEU D 137 SER D 141 5 5 HELIX 9 9 TYR B 54 ASN B 68 1 15 HELIX 10 10 VAL B 99 GLN B 106 1 8 HELIX 11 11 HIS B 121 GLU B 135 1 15 HELIX 12 12 LEU B 137 SER B 141 5 5 HELIX 13 13 TYR C 54 ASN C 68 1 15 HELIX 14 14 VAL C 99 GLN C 106 1 8 HELIX 15 15 HIS C 121 GLU C 135 1 15 HELIX 16 16 LEU C 137 SER C 141 5 5 SHEET 1 A 5 LYS A 9 ALA A 12 0 SHEET 2 A 5 ILE D 72 PHE D 76 -1 O VAL D 74 N GLU A 10 SHEET 3 A 5 GLY D 88 ALA D 94 -1 O TYR D 91 N GLU D 75 SHEET 4 A 5 GLN D 30 LEU D 36 1 N ARG D 35 O GLY D 88 SHEET 5 A 5 THR D 22 TYR D 27 -1 N TYR D 27 O GLN D 30 SHEET 1 B 4 LYS A 9 ALA A 12 0 SHEET 2 B 4 ILE D 72 PHE D 76 -1 O VAL D 74 N GLU A 10 SHEET 3 B 4 GLY D 88 ALA D 94 -1 O TYR D 91 N GLU D 75 SHEET 4 B 4 LYS D 97 MET D 98 -1 O LYS D 97 N ALA D 94 SHEET 1 C 4 THR A 22 TYR A 27 0 SHEET 2 C 4 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 3 C 4 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 4 C 4 LYS A 97 MET A 98 -1 O LYS A 97 N ALA A 94 SHEET 1 D 5 THR A 22 TYR A 27 0 SHEET 2 D 5 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 3 D 5 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 4 D 5 ILE A 72 PHE A 76 -1 N GLU A 73 O TYR A 93 SHEET 5 D 5 GLU D 10 ALA D 12 -1 O GLU D 10 N VAL A 74 SHEET 1 E 2 VAL A 39 ASP A 40 0 SHEET 2 E 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 SHEET 1 F 2 VAL D 39 ASP D 40 0 SHEET 2 F 2 LYS D 110 VAL D 111 -1 O LYS D 110 N ASP D 40 SHEET 1 G 5 LYS B 9 ALA B 12 0 SHEET 2 G 5 ILE C 72 PHE C 76 -1 O VAL C 74 N GLU B 10 SHEET 3 G 5 GLY C 88 ALA C 94 -1 O TYR C 91 N GLU C 75 SHEET 4 G 5 GLN C 30 LEU C 36 1 N ARG C 35 O GLY C 88 SHEET 5 G 5 THR C 22 TYR C 27 -1 N TYR C 27 O GLN C 30 SHEET 1 H 4 LYS B 9 ALA B 12 0 SHEET 2 H 4 ILE C 72 PHE C 76 -1 O VAL C 74 N GLU B 10 SHEET 3 H 4 GLY C 88 ALA C 94 -1 O TYR C 91 N GLU C 75 SHEET 4 H 4 LYS C 97 MET C 98 -1 O LYS C 97 N ALA C 94 SHEET 1 I 4 THR B 22 TYR B 27 0 SHEET 2 I 4 GLN B 30 LEU B 36 -1 O PHE B 34 N VAL B 23 SHEET 3 I 4 GLY B 88 ALA B 94 1 O GLY B 88 N ARG B 35 SHEET 4 I 4 LYS B 97 MET B 98 -1 O LYS B 97 N ALA B 94 SHEET 1 J 5 THR B 22 TYR B 27 0 SHEET 2 J 5 GLN B 30 LEU B 36 -1 O PHE B 34 N VAL B 23 SHEET 3 J 5 GLY B 88 ALA B 94 1 O GLY B 88 N ARG B 35 SHEET 4 J 5 ILE B 72 PHE B 76 -1 N GLU B 75 O TYR B 91 SHEET 5 J 5 GLU C 10 ALA C 12 -1 O GLU C 10 N VAL B 74 SHEET 1 K 2 VAL B 39 ASP B 40 0 SHEET 2 K 2 LYS B 110 VAL B 111 -1 O LYS B 110 N ASP B 40 SHEET 1 L 2 VAL C 39 ASP C 40 0 SHEET 2 L 2 LYS C 110 VAL C 111 -1 O LYS C 110 N ASP C 40 SITE 1 AC1 14 ARG A 35 LYS A 84 TYR A 85 ARG A 87 SITE 2 AC1 14 LEU A 89 TYR A 113 HOH A 155 HOH A 159 SITE 3 AC1 14 HOH A 160 HOH A 166 HOH A 200 HOH A 203 SITE 4 AC1 14 HOH A 232 HOH A 245 SITE 1 AC2 14 ARG B 35 HOH B 45 LYS B 84 TYR B 85 SITE 2 AC2 14 ARG B 87 LEU B 89 TYR B 113 HOH B 153 SITE 3 AC2 14 HOH B 154 HOH B 163 HOH B 164 HOH B 178 SITE 4 AC2 14 HOH B 208 HOH B 209 SITE 1 AC3 14 ARG C 35 LYS C 84 TYR C 85 ARG C 87 SITE 2 AC3 14 LEU C 89 TYR C 113 HOH C 152 HOH C 158 SITE 3 AC3 14 HOH C 179 HOH C 195 HOH C 200 HOH C 228 SITE 4 AC3 14 HOH C 267 HOH C 296 SITE 1 AC4 10 ARG D 35 LYS D 84 TYR D 85 ARG D 87 SITE 2 AC4 10 LEU D 89 HOH D 155 HOH D 159 HOH D 161 SITE 3 AC4 10 HOH D 191 HOH D 231 SITE 1 AC5 4 GLN B 80 LYS B 116 ASN B 118 GLN D 106 SITE 1 AC6 7 GLN A 80 TYR A 115 LYS A 116 ASN A 118 SITE 2 AC6 7 HOH A 238 GLN C 106 LEU C 137 SITE 1 AC7 4 MET B 26 THR C 13 HOH C 221 HOH C 223 SITE 1 AC8 5 LYS A 116 HOH A 212 HOH A 213 HOH A 215 SITE 2 AC8 5 HOH C 215 CRYST1 67.598 74.420 67.975 90.00 90.22 90.00 P 1 21 1 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 0.014793 0.000000 0.000056 0.00000 SCALE2 0.000000 0.013437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014711 0.00000