HEADER HYDROLASE 18-JUN-10 3NK9 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS V74A AT TITLE 2 CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEASE A; 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: 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, HYDROLASE, PDTP, KEYWDS 2 CAVITY, PRESSURE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,J.L.SCHLESSMAN,B.GARCIA-MORENO E.,A.HEROUX REVDAT 4 06-SEP-23 3NK9 1 REMARK SEQADV LINK REVDAT 3 30-MAY-12 3NK9 1 JRNL REVDAT 2 25-APR-12 3NK9 1 JRNL VERSN REVDAT 1 29-JUN-11 3NK9 0 JRNL AUTH J.ROCHE,J.A.CARO,D.R.NORBERTO,P.BARTHE,C.ROUMESTAND, JRNL AUTH 2 J.L.SCHLESSMAN,A.E.GARCIA,B.GARCIA-MORENO E,C.A.ROYER JRNL TITL CAVITIES DETERMINE THE PRESSURE UNFOLDING OF PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 6945 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22496593 JRNL DOI 10.1073/PNAS.1200915109 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15112 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1677 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1086 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1031 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.90000 REMARK 3 B22 (A**2) : -1.69000 REMARK 3 B33 (A**2) : 3.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.930 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1103 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1493 ; 1.611 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 138 ; 6.418 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 47 ;34.666 ;24.894 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 216 ;15.413 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;12.275 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 163 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 801 ; 0.013 ; 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): 654 ; 1.318 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1052 ; 1.915 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 449 ; 3.039 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 436 ; 4.398 ; 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 27 REMARK 3 ORIGIN FOR THE GROUP (A): 13.2229 -3.8401 3.6761 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.0599 REMARK 3 T33: 0.0891 T12: 0.0277 REMARK 3 T13: -0.0151 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.6660 L22: 2.5275 REMARK 3 L33: 0.8087 L12: 0.2396 REMARK 3 L13: -0.5467 L23: 1.1644 REMARK 3 S TENSOR REMARK 3 S11: -0.1167 S12: -0.0654 S13: -0.2224 REMARK 3 S21: 0.0864 S22: 0.0761 S23: -0.0523 REMARK 3 S31: 0.1124 S32: 0.0689 S33: 0.0407 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 28 A 36 REMARK 3 ORIGIN FOR THE GROUP (A): 16.5677 -2.1569 0.7781 REMARK 3 T TENSOR REMARK 3 T11: 0.0638 T22: 0.0753 REMARK 3 T33: 0.2253 T12: 0.0169 REMARK 3 T13: 0.0330 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 2.8273 L22: 9.0938 REMARK 3 L33: 0.9706 L12: -5.0063 REMARK 3 L13: -1.1104 L23: 2.2190 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: 0.0703 S13: -0.0569 REMARK 3 S21: 0.0126 S22: -0.0342 S23: -0.0640 REMARK 3 S31: 0.1141 S32: -0.0023 S33: 0.0036 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 37 A 63 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4306 6.1959 13.8618 REMARK 3 T TENSOR REMARK 3 T11: 0.1260 T22: 0.1568 REMARK 3 T33: 0.0165 T12: 0.0307 REMARK 3 T13: -0.0152 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 3.0335 L22: 2.5906 REMARK 3 L33: 1.4446 L12: 0.1030 REMARK 3 L13: -0.2876 L23: 0.4310 REMARK 3 S TENSOR REMARK 3 S11: -0.0808 S12: -0.5750 S13: 0.0999 REMARK 3 S21: 0.4419 S22: 0.0824 S23: -0.0806 REMARK 3 S31: 0.0611 S32: 0.1597 S33: -0.0015 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 64 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8379 4.8742 0.8960 REMARK 3 T TENSOR REMARK 3 T11: 0.0727 T22: 0.0725 REMARK 3 T33: 0.0463 T12: -0.0091 REMARK 3 T13: 0.0023 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 2.4282 L22: 2.5325 REMARK 3 L33: 0.5335 L12: -0.6517 REMARK 3 L13: 0.0529 L23: 0.4872 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: 0.1462 S13: -0.0093 REMARK 3 S21: -0.0790 S22: 0.0253 S23: 0.1233 REMARK 3 S31: 0.0363 S32: -0.0208 S33: -0.0132 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 118 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8219 15.2072 11.0539 REMARK 3 T TENSOR REMARK 3 T11: 0.0753 T22: 0.0708 REMARK 3 T33: 0.1371 T12: 0.0359 REMARK 3 T13: 0.0470 T23: -0.0406 REMARK 3 L TENSOR REMARK 3 L11: 4.5170 L22: 2.8034 REMARK 3 L33: 4.0352 L12: 0.1492 REMARK 3 L13: 1.7209 L23: 0.5405 REMARK 3 S TENSOR REMARK 3 S11: -0.2220 S12: -0.5179 S13: 0.4817 REMARK 3 S21: 0.3412 S22: 0.1314 S23: 0.4114 REMARK 3 S31: -0.2574 S32: -0.0651 S33: 0.0906 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 3NK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059934. 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) : 1.1000 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 : 16836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.18300 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: 3BDC WITH ALL H2OS, CA2+ AND THP REMOVED AND THE REMARK 200 FOLLOWING TRUNCATIONS: H8A, T13A, Q30A, K64A, V74A, T82A, Y113A, REMARK 200 V114A AND Y115A; ALL B-FACTORS WERE RESET TO 20 A^2. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% 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 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 30.21750 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: 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 -1.65 67.38 REMARK 500 ASN A 118 56.49 -115.27 REMARK 500 ASN A 138 -102.94 48.81 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 81.3 REMARK 620 3 THR A 41 O 87.1 75.4 REMARK 620 4 GLU A 43 OE2 155.1 123.0 103.1 REMARK 620 5 THP A 150 O4P 95.1 71.4 146.0 89.0 REMARK 620 6 HOH A 159 O 80.6 137.2 65.2 83.2 148.6 REMARK 620 7 HOH A 165 O 77.5 138.4 137.7 79.9 75.3 73.4 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS REMARK 900 RELATED ID: 3MEH RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS VARIANT I92A REMARK 900 RELATED ID: 3MHB RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS VARIANT L38A REMARK 900 RELATED ID: 3MXP RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS VARIANT T62A REMARK 900 RELATED ID: 3MVV RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS VARIANT F34A REMARK 900 RELATED ID: 3MZ5 RELATED DB: PDB REMARK 900 STAPH NUCLEASE DELTA+PHS VARIANT L103A DBREF 3NK9 A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3NK9 A UNP P00644 THR 126 DELETION SEQADV 3NK9 A UNP P00644 LYS 127 DELETION SEQADV 3NK9 A UNP P00644 HIS 128 DELETION SEQADV 3NK9 A UNP P00644 PRO 129 DELETION SEQADV 3NK9 A UNP P00644 LYS 130 DELETION SEQADV 3NK9 A UNP P00644 LYS 131 DELETION SEQADV 3NK9 PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3NK9 ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3NK9 ALA A 74 UNP P00644 VAL 156 ENGINEERED MUTATION SEQADV 3NK9 GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3NK9 LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3NK9 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 ALA 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 HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 2 THP C10 H16 N2 O11 P2 FORMUL 3 CA CA 2+ FORMUL 4 HOH *76(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 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 75 O TYR A 91 SHEET 4 A 7 LYS A 9 ALA A 17 -1 N GLU A 10 O ALA A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O MET A 26 N THR A 13 SHEET 6 A 7 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL 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 151 1555 1555 2.84 LINK OD1 ASP A 40 CA CA A 151 1555 1555 2.75 LINK O THR A 41 CA CA A 151 1555 1555 2.85 LINK OE2 GLU A 43 CA CA A 151 1555 1555 3.05 LINK O4P THP A 150 CA CA A 151 1555 1555 3.08 LINK CA CA A 151 O HOH A 159 1555 1555 2.86 LINK CA CA A 151 O HOH A 165 1555 1555 2.82 SITE 1 AC1 22 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC1 22 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC1 22 LYS A 127 CA A 151 HOH A 158 HOH A 164 SITE 4 AC1 22 HOH A 165 HOH A 176 HOH A 178 HOH A 180 SITE 5 AC1 22 HOH A 181 HOH A 191 HOH A 196 HOH A 201 SITE 6 AC1 22 HOH A 218 HOH A 220 SITE 1 AC2 7 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC2 7 THP A 150 HOH A 159 HOH A 165 CRYST1 31.075 60.435 38.129 90.00 93.30 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 0.032180 0.000000 0.001855 0.00000 SCALE2 0.000000 0.016547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026270 0.00000