HEADER HYDROLASE 17-SEP-10 3OWF TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS V66R AT TITLE 2 CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.31.1; COMPND 5 ENGINEERED: YES; COMPND 6 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 EXPDTA X-RAY DIFFRACTION AUTHOR J.L.SCHLESSMAN,V.KHANGULOV,A.HEROUX,B.GARCIA-MORENO E. REVDAT 2 06-SEP-23 3OWF 1 REMARK SEQADV LINK REVDAT 1 20-OCT-10 3OWF 0 JRNL AUTH J.L.SCHLESSMAN,V.KHANGULOV,A.HEROUX,B.GARCIA-MORENO E. 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 16308 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 868 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1157 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1080 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -0.87000 REMARK 3 B12 (A**2) : 0.29000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.507 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1213 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1646 ; 1.693 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 155 ; 5.291 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;33.819 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 251 ;15.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;10.793 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 177 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 880 ; 0.014 ; 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): 705 ; 1.510 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1143 ; 2.250 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 508 ; 3.814 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 491 ; 5.559 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 16 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0590 -39.9190 7.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.1598 T22: 0.1484 REMARK 3 T33: 0.0272 T12: -0.1227 REMARK 3 T13: 0.0615 T23: -0.0488 REMARK 3 L TENSOR REMARK 3 L11: 18.9193 L22: 8.7381 REMARK 3 L33: 3.3111 L12: 11.4280 REMARK 3 L13: -7.8515 L23: -5.0488 REMARK 3 S TENSOR REMARK 3 S11: 0.8788 S12: -0.8336 S13: 0.5187 REMARK 3 S21: 0.5631 S22: -0.6482 S23: 0.2725 REMARK 3 S31: -0.3883 S32: 0.3795 S33: -0.2306 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 17 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 28.2160 -25.6980 -3.7320 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.1109 REMARK 3 T33: 0.0679 T12: -0.0104 REMARK 3 T13: 0.0436 T23: 0.0283 REMARK 3 L TENSOR REMARK 3 L11: 2.5117 L22: 2.2639 REMARK 3 L33: 2.5207 L12: 0.7751 REMARK 3 L13: -0.6147 L23: -0.5247 REMARK 3 S TENSOR REMARK 3 S11: 0.0502 S12: 0.1268 S13: 0.0325 REMARK 3 S21: 0.2567 S22: 0.0608 S23: 0.2992 REMARK 3 S31: 0.0290 S32: -0.2834 S33: -0.1110 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 60 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): 34.2000 -17.6200 -6.4830 REMARK 3 T TENSOR REMARK 3 T11: 0.0728 T22: 0.0525 REMARK 3 T33: 0.0515 T12: -0.0024 REMARK 3 T13: 0.0193 T23: 0.0304 REMARK 3 L TENSOR REMARK 3 L11: 1.3674 L22: 2.1922 REMARK 3 L33: 2.7825 L12: 0.3750 REMARK 3 L13: -0.1149 L23: 0.0610 REMARK 3 S TENSOR REMARK 3 S11: -0.0346 S12: 0.1182 S13: 0.2328 REMARK 3 S21: 0.2034 S22: 0.1185 S23: 0.1815 REMARK 3 S31: -0.2264 S32: -0.0872 S33: -0.0840 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 4 REMARK 4 3OWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.1000 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 MONOCHROMATOR WITH CRYOGENICALLY- REMARK 200 COOLED FIRST CRYSTAL AND REMARK 200 SAGITTALLY-BENT SECOND CRYSTAL REMARK 200 HORIZONTALLY-FOCUSING AT 3.3:1 REMARK 200 DEMAGNIFICATION. REMARK 200 OPTICS : MERIDIONALLY-BENT FUSED SILICA REMARK 200 MIRROR WITH PALLADIUM AND REMARK 200 UNCOATED STRIPES VERTICALLY- REMARK 200 FOCUSING AT 6.6:1 REMARK 200 DEMAGNIFICATION. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17185 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 21.40 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.40 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 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 2.1.4 REMARK 200 STARTING MODEL: PDB ID: 3BDC RESIDUES 21-141. ALL B-FACTORS WERE REMARK 200 SET TO 20 A^2. ARG-66, PHE-113, VAL-114, PHE-115, LYS-116 WERE REMARK 200 TRUNCATED TO ALA. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 25.71333 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 12.85667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.85667 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 25.71333 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 ASYMMETRIC UNIT CONTAINS ONE MONOMER WHOSE N-TERMINUS REMARK 300 HAS REARRANGED TO WRAP AROUND A SYMMETRY-RELATED MOLECULE, CREATING REMARK 300 A DOMAIN-SWAPPED DIMERIC ASSEMBLY. 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: 4160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -12.85667 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 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 ASP A 19 137.97 -37.63 REMARK 500 TYR A 54 -3.09 75.29 REMARK 500 ASP A 95 53.94 38.48 REMARK 500 ASN A 138 -107.13 48.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 151 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 84.9 REMARK 620 3 THR A 41 O 90.4 75.5 REMARK 620 4 THP A 150 O5P 98.7 77.4 150.5 REMARK 620 5 HOH A 203 O 77.0 146.0 132.4 77.2 REMARK 620 6 HOH A 205 O 168.7 91.1 78.4 90.7 111.5 REMARK 620 7 HOH A 211 O 91.3 141.1 65.8 141.2 68.8 85.2 REMARK 620 N 1 2 3 4 5 6 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 CA A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 152 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS REMARK 900 RELATED ID: 3HEJ RELATED DB: PDB REMARK 900 STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS T62R DBREF 3OWF A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3OWF A UNP P00644 THR 126 DELETION SEQADV 3OWF A UNP P00644 LYS 127 DELETION SEQADV 3OWF A UNP P00644 HIS 128 DELETION SEQADV 3OWF A UNP P00644 PRO 129 DELETION SEQADV 3OWF A UNP P00644 LYS 130 DELETION SEQADV 3OWF A UNP P00644 LYS 131 DELETION SEQADV 3OWF PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3OWF ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3OWF ARG A 66 UNP P00644 VAL 148 ENGINEERED MUTATION SEQADV 3OWF GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3OWF LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3OWF ALA A 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 THR LYS LYS MET ARG 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 HET THP A 150 25 HET CA A 151 1 HET PO4 A 152 5 HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 2 THP C10 H16 N2 O11 P2 FORMUL 3 CA CA 2+ FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *111(H2 O) HELIX 1 1 ALA A 1 LYS A 5 5 5 HELIX 2 2 TYR A 54 ALA A 69 1 16 HELIX 3 3 VAL A 99 GLN A 106 1 8 HELIX 4 4 HIS A 121 GLU A 135 1 15 HELIX 5 5 LEU A 137 SER A 141 5 5 SHEET 1 A 4 THR A 22 TYR A 27 0 SHEET 2 A 4 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 3 A 4 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 4 A 4 ILE A 72 GLU A 75 -1 N GLU A 73 O TYR A 93 SHEET 1 B 4 THR A 22 TYR A 27 0 SHEET 2 B 4 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 3 B 4 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 4 B 4 LYS A 97 MET A 98 -1 O LYS A 97 N ALA A 94 SHEET 1 C 2 VAL A 39 ASP A 40 0 SHEET 2 C 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK OD2 ASP A 21 CA CA A 151 1555 1555 2.44 LINK OD1 ASP A 40 CA CA A 151 1555 1555 2.33 LINK O THR A 41 CA CA A 151 1555 1555 2.67 LINK O5P THP A 150 CA CA A 151 1555 1555 2.52 LINK CA CA A 151 O HOH A 203 1555 1555 2.55 LINK CA CA A 151 O HOH A 205 1555 1555 2.37 LINK CA CA A 151 O HOH A 211 1555 1555 2.58 SITE 1 AC1 20 ALA A 1 THR A 4 LYS A 5 ARG A 35 SITE 2 AC1 20 ASP A 40 LYS A 78 LYS A 84 TYR A 85 SITE 3 AC1 20 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 4 AC1 20 LYS A 116 CA A 151 HOH A 202 HOH A 203 SITE 5 AC1 20 HOH A 208 HOH A 223 HOH A 241 HOH A 244 SITE 1 AC2 7 ASP A 21 ASP A 40 THR A 41 THP A 150 SITE 2 AC2 7 HOH A 203 HOH A 205 HOH A 211 SITE 1 AC3 3 LYS A 63 ARG A 66 GLU A 67 CRYST1 94.509 94.509 38.570 90.00 90.00 120.00 P 32 2 1 6 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 0.010581 0.006109 0.000000 0.00000 SCALE2 0.000000 0.012218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025927 0.00000