HEADER HYDROLASE 10-FEB-11 3QOJ TITLE CRYOGENIC STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS/V23K COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEASE A (UNP RESIDUES 83-231); COMPND 5 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE; 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: 469008; 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, PDTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.ROBINSON,J.L.SCHLESSMAN,A.HEROUX,B.GARCIA-MORENO E. REVDAT 2 13-SEP-23 3QOJ 1 REMARK SEQADV LINK REVDAT 1 16-MAR-11 3QOJ 0 JRNL AUTH A.C.ROBINSON,J.L.SCHLESSMAN,A.HEROUX,B.GARCIA-MORENO E., JRNL AUTH 2 C.A.CASTANEDA JRNL TITL DETERMINANTS OF PKA VALUES OF INTERNAL IONIZABLE GROUPS: JRNL TITL 2 PROPERTIES OF ION PAIRS IN THE PROTEIN CORE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 18219 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 937 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) : 1331 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1035 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : 0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.301 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1091 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1468 ; 1.819 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 130 ; 6.460 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;32.339 ;24.792 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 212 ;14.477 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 7.137 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 795 ; 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): 645 ; 1.479 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1031 ; 2.330 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 446 ; 3.448 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 437 ; 5.119 ; 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 : 6 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 7 A 11 REMARK 3 ORIGIN FOR THE GROUP (A): 36.5240 7.1560 -5.0730 REMARK 3 T TENSOR REMARK 3 T11: 0.1213 T22: 0.1234 REMARK 3 T33: 0.1706 T12: 0.0067 REMARK 3 T13: -0.0336 T23: -0.0682 REMARK 3 L TENSOR REMARK 3 L11: 1.1494 L22: 5.1831 REMARK 3 L33: 0.4959 L12: 1.2413 REMARK 3 L13: 1.7172 L23: -0.6624 REMARK 3 S TENSOR REMARK 3 S11: -0.1391 S12: 0.2862 S13: -0.4266 REMARK 3 S21: -0.1833 S22: 0.1292 S23: 0.2854 REMARK 3 S31: -0.0574 S32: -0.0077 S33: 0.0099 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 12 A 38 REMARK 3 ORIGIN FOR THE GROUP (A): 46.9150 10.3650 3.9140 REMARK 3 T TENSOR REMARK 3 T11: 0.1318 T22: 0.1092 REMARK 3 T33: 0.0993 T12: 0.0196 REMARK 3 T13: -0.0158 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.8620 L22: 1.1892 REMARK 3 L33: -0.0963 L12: -0.1709 REMARK 3 L13: -0.3374 L23: 0.4196 REMARK 3 S TENSOR REMARK 3 S11: -0.0567 S12: -0.0489 S13: -0.0570 REMARK 3 S21: 0.0424 S22: 0.0900 S23: -0.1244 REMARK 3 S31: -0.0009 S32: 0.0213 S33: -0.0333 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 39 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 41.4840 15.6120 9.5570 REMARK 3 T TENSOR REMARK 3 T11: 0.1743 T22: 0.1299 REMARK 3 T33: 0.0000 T12: 0.0069 REMARK 3 T13: -0.0042 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 2.4768 L22: 1.0504 REMARK 3 L33: -0.3982 L12: -0.9468 REMARK 3 L13: -0.3025 L23: 0.4507 REMARK 3 S TENSOR REMARK 3 S11: -0.1725 S12: -0.2274 S13: -0.0426 REMARK 3 S21: 0.1522 S22: 0.1535 S23: 0.0619 REMARK 3 S31: 0.0538 S32: 0.0944 S33: 0.0190 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 81 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 39.8350 15.9980 3.0780 REMARK 3 T TENSOR REMARK 3 T11: 0.1141 T22: 0.1169 REMARK 3 T33: 0.0813 T12: -0.0096 REMARK 3 T13: 0.0050 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.4448 L22: 1.8424 REMARK 3 L33: -0.5624 L12: -0.4232 REMARK 3 L13: 0.1286 L23: -0.1083 REMARK 3 S TENSOR REMARK 3 S11: -0.0800 S12: 0.0397 S13: -0.0466 REMARK 3 S21: 0.0318 S22: 0.1058 S23: 0.0839 REMARK 3 S31: 0.0433 S32: 0.0086 S33: -0.0258 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 107 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 37.4310 24.6640 -0.6130 REMARK 3 T TENSOR REMARK 3 T11: 0.1238 T22: 0.1091 REMARK 3 T33: 0.0845 T12: -0.0072 REMARK 3 T13: -0.0278 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 1.8010 L22: 2.1756 REMARK 3 L33: -0.4297 L12: -0.8569 REMARK 3 L13: -0.5706 L23: 0.4075 REMARK 3 S TENSOR REMARK 3 S11: 0.0267 S12: 0.1328 S13: 0.2547 REMARK 3 S21: -0.1597 S22: 0.0022 S23: 0.1498 REMARK 3 S31: -0.0991 S32: -0.0217 S33: -0.0290 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 124 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 30.2750 27.3660 11.0870 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.1070 REMARK 3 T33: 0.2107 T12: 0.0327 REMARK 3 T13: 0.0790 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 1.6342 L22: 1.9077 REMARK 3 L33: 1.4736 L12: -0.6277 REMARK 3 L13: 0.8834 L23: 0.1426 REMARK 3 S TENSOR REMARK 3 S11: -0.2275 S12: -0.1568 S13: 0.2021 REMARK 3 S21: 0.2508 S22: 0.2141 S23: 0.5919 REMARK 3 S31: -0.0285 S32: 0.1063 S33: 0.0135 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 3QOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.9795 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 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18219 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 23.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4000 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) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25200 REMARK 200 FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3BDC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 PDTP (2 EQ.), CALCIUM CHLORIDE (3 EQ.), PH 8, 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 30.17550 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 125 CB - CG - CD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 54 -2.13 66.33 REMARK 500 ASN A 138 -107.64 51.00 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 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 81.6 REMARK 620 3 THR A 41 O 87.6 76.2 REMARK 620 4 GLU A 43 OE1 153.7 123.5 104.6 REMARK 620 5 HOH A 45 O 81.7 139.1 66.0 82.3 REMARK 620 6 THP A 151 O5P 95.4 69.2 144.4 88.0 149.5 REMARK 620 7 HOH A 181 O 77.0 137.3 138.2 78.6 73.4 76.4 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 CA A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT D+PHS REMARK 900 RELATED ID: 3NHH RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT D+PHS/V23E/L36K DBREF 3QOJ A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3QOJ LYS A 23 UNP P00644 VAL 105 ENGINEERED MUTATION SEQADV 3QOJ A UNP P00644 THR 126 DELETION SEQADV 3QOJ A UNP P00644 LYS 127 DELETION SEQADV 3QOJ A UNP P00644 HIS 128 DELETION SEQADV 3QOJ A UNP P00644 PRO 129 DELETION SEQADV 3QOJ A UNP P00644 LYS 130 DELETION SEQADV 3QOJ A UNP P00644 LYS 131 DELETION SEQADV 3QOJ PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3QOJ ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3QOJ GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3QOJ LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3QOJ 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 LYS 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 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 HET CA A 150 1 HET THP A 151 25 HETNAM CA CALCIUM ION HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 THP C10 H16 N2 O11 P2 FORMUL 4 HOH *111(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 SHEET 1 A 7 LYS A 97 MET A 98 0 SHEET 2 A 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 A 7 ILE A 72 GLU A 75 -1 N GLU A 73 O TYR A 93 SHEET 4 A 7 LYS A 9 ALA A 17 -1 N GLU A 10 O VAL A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O LYS A 24 N LYS A 16 SHEET 6 A 7 GLN A 30 LEU A 36 -1 O PHE A 34 N LYS A 23 SHEET 7 A 7 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 1 B 2 VAL A 39 ASP A 40 0 SHEET 2 B 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK OD2 ASP A 21 CA CA A 150 1555 1555 2.86 LINK OD1 ASP A 40 CA CA A 150 1555 1555 2.66 LINK O THR A 41 CA CA A 150 1555 1555 2.88 LINK OE1 GLU A 43 CA CA A 150 1555 1555 3.01 LINK O HOH A 45 CA CA A 150 1555 1555 2.90 LINK CA CA A 150 O5P THP A 151 1555 1555 3.17 LINK CA CA A 150 O HOH A 181 1555 1555 2.78 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC1 7 HOH A 45 THP A 151 HOH A 181 SITE 1 AC2 20 ARG A 35 ASP A 40 HOH A 48 LYS A 84 SITE 2 AC2 20 TYR A 85 ARG A 87 TYR A 113 TYR A 115 SITE 3 AC2 20 LYS A 127 CA A 150 HOH A 152 HOH A 156 SITE 4 AC2 20 HOH A 173 HOH A 181 HOH A 192 HOH A 215 SITE 5 AC2 20 HOH A 220 HOH A 227 HOH A 229 HOH A 247 CRYST1 31.138 60.351 38.156 90.00 93.86 90.00 P 1 21 1 2 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 0.032115 0.000000 0.002168 0.00000 SCALE2 0.000000 0.016570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026268 0.00000