HEADER HYDROLASE 05-MAY-11 3RUZ TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS V74K AT TITLE 2 CRYOGENIC TEMPERATURE 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, CAVITY, PRESSURE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,I.CLARK,A.HEROUX,J.L.SCHLESSMAN,B.GARCIA-MORENO E. REVDAT 2 13-SEP-23 3RUZ 1 REMARK SEQADV LINK REVDAT 1 15-JUN-11 3RUZ 0 JRNL AUTH J.A.CARO,J.L.SCHLESSMAN,B.GARCIA-MORENO E. JRNL TITL INTERNAL IONIZABLE RESIDUES IN PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20316 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2068 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1258 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3160 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 : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : 0.50000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.559 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1122 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1518 ; 1.675 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 141 ; 6.917 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;33.530 ;25.200 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 225 ;15.157 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;13.403 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 164 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 817 ; 0.015 ; 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): 659 ; 1.438 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1061 ; 2.229 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 463 ; 3.786 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 450 ; 5.938 ; 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 : 5 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 24 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2107 -3.8037 -13.9756 REMARK 3 T TENSOR REMARK 3 T11: 0.0431 T22: 0.0389 REMARK 3 T33: 0.0510 T12: 0.0023 REMARK 3 T13: 0.0046 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.3845 L22: 2.0773 REMARK 3 L33: 0.7691 L12: 0.3827 REMARK 3 L13: -0.0840 L23: -0.2065 REMARK 3 S TENSOR REMARK 3 S11: -0.0096 S12: -0.0336 S13: 0.0330 REMARK 3 S21: -0.0121 S22: 0.0000 S23: 0.0599 REMARK 3 S31: -0.1055 S32: 0.0142 S33: 0.0095 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 25 A 42 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9031 -6.9475 -16.3743 REMARK 3 T TENSOR REMARK 3 T11: 0.0415 T22: 0.0377 REMARK 3 T33: 0.0454 T12: 0.0007 REMARK 3 T13: -0.0031 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 1.2293 L22: 2.3439 REMARK 3 L33: 0.2309 L12: -0.7198 REMARK 3 L13: -0.1507 L23: 0.2845 REMARK 3 S TENSOR REMARK 3 S11: 0.0170 S12: 0.0359 S13: 0.0523 REMARK 3 S21: -0.0872 S22: -0.0135 S23: 0.0923 REMARK 3 S31: -0.0684 S32: -0.0648 S33: -0.0035 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 43 A 71 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9293 -11.5116 -3.4116 REMARK 3 T TENSOR REMARK 3 T11: 0.0726 T22: 0.0672 REMARK 3 T33: 0.0349 T12: 0.0242 REMARK 3 T13: 0.0223 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.1032 L22: 2.9774 REMARK 3 L33: 2.8597 L12: 0.6300 REMARK 3 L13: -0.3215 L23: -1.0415 REMARK 3 S TENSOR REMARK 3 S11: -0.0999 S12: -0.1738 S13: -0.0018 REMARK 3 S21: 0.1531 S22: 0.0722 S23: 0.0547 REMARK 3 S31: -0.0087 S32: -0.0572 S33: 0.0276 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 72 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7346 -7.3548 -19.4945 REMARK 3 T TENSOR REMARK 3 T11: 0.0681 T22: 0.0471 REMARK 3 T33: 0.0458 T12: -0.0024 REMARK 3 T13: 0.0000 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.5426 L22: 2.2938 REMARK 3 L33: 1.0932 L12: 0.1975 REMARK 3 L13: -0.2482 L23: -0.0234 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: 0.1385 S13: 0.0559 REMARK 3 S21: -0.1296 S22: 0.0065 S23: 0.0771 REMARK 3 S31: -0.0335 S32: -0.0122 S33: 0.0016 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 100 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 13.4028 -20.6838 -13.9393 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.0405 REMARK 3 T33: 0.0489 T12: 0.0073 REMARK 3 T13: 0.0086 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.2393 L22: 1.7950 REMARK 3 L33: 1.2746 L12: -0.1531 REMARK 3 L13: -0.1531 L23: 0.2294 REMARK 3 S TENSOR REMARK 3 S11: -0.0091 S12: 0.0250 S13: -0.0488 REMARK 3 S21: -0.0072 S22: 0.0289 S23: -0.0087 REMARK 3 S31: 0.1106 S32: 0.0765 S33: -0.0198 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 3RUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065409. 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 : 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) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20367 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 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 2.2.1 REMARK 200 STARTING MODEL: PDB ENTRY 3BDC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 16.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.27250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.13150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.27250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.13150 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 127 O1P THP A 151 1655 2.14 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 -2.82 72.32 REMARK 500 ASN A 138 -108.54 47.71 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 86.6 REMARK 620 3 THR A 41 O 87.6 81.2 REMARK 620 4 HOH A 161 O 73.2 138.2 132.3 REMARK 620 5 HOH A 177 O 78.6 142.5 64.0 69.5 REMARK 620 6 HOH A 223 O 151.8 106.4 118.6 80.8 102.6 REMARK 620 N 1 2 3 4 5 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 DELTA+PHS REMARK 900 RELATED ID: 3NK9 RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS V74A REMARK 900 RELATED ID: 3P1H RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS V23K/I92A REMARK 900 RELATED ID: 3QB3 RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS I92K/L25A DBREF 3RUZ A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3RUZ A UNP P00644 THR 126 DELETION SEQADV 3RUZ A UNP P00644 LYS 127 DELETION SEQADV 3RUZ A UNP P00644 HIS 128 DELETION SEQADV 3RUZ A UNP P00644 PRO 129 DELETION SEQADV 3RUZ A UNP P00644 LYS 130 DELETION SEQADV 3RUZ A UNP P00644 LYS 131 DELETION SEQADV 3RUZ PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3RUZ ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3RUZ LYS A 74 UNP P00644 VAL 156 ENGINEERED MUTATION SEQADV 3RUZ GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3RUZ LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3RUZ 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 VAL GLU ASN ALA LYS LYS SEQRES 6 A 143 ILE GLU LYS 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 *134(H2 O) HELIX 1 1 TYR A 54 ALA A 69 1 16 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 6 GLU A 10 ALA A 12 0 SHEET 2 A 6 ILE A 72 GLU A 75 -1 O LYS A 74 N GLU A 10 SHEET 3 A 6 GLY A 88 ALA A 94 -1 O TYR A 93 N GLU A 73 SHEET 4 A 6 GLN A 30 LEU A 36 1 N ARG A 35 O GLY A 88 SHEET 5 A 6 THR A 22 TYR A 27 -1 N VAL A 23 O PHE A 34 SHEET 6 A 6 LEU A 14 ALA A 17 -1 N LYS A 16 O LYS A 24 SHEET 1 B 4 GLU A 10 ALA A 12 0 SHEET 2 B 4 ILE A 72 GLU A 75 -1 O LYS A 74 N GLU A 10 SHEET 3 B 4 GLY A 88 ALA A 94 -1 O TYR A 93 N GLU A 73 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 150 1555 1555 2.87 LINK OD1 ASP A 40 CA CA A 150 1555 1555 2.67 LINK O THR A 41 CA CA A 150 1555 1555 2.77 LINK CA CA A 150 O HOH A 161 1555 1555 2.86 LINK CA CA A 150 O HOH A 177 1555 1555 3.03 LINK CA CA A 150 O HOH A 223 1555 1555 2.78 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 THP A 151 SITE 2 AC1 7 HOH A 161 HOH A 177 HOH A 223 SITE 1 AC2 21 ARG A 35 ASP A 40 ASP A 83 LYS A 84 SITE 2 AC2 21 TYR A 85 ARG A 87 LEU A 89 TYR A 113 SITE 3 AC2 21 LYS A 127 CA A 150 HOH A 158 HOH A 161 SITE 4 AC2 21 HOH A 163 HOH A 172 HOH A 182 HOH A 188 SITE 5 AC2 21 HOH A 196 HOH A 213 HOH A 223 HOH A 240 SITE 6 AC2 21 HOH A 262 CRYST1 32.000 60.263 74.545 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 0.031250 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013415 0.00000