HEADER HYDROLASE 24-APR-13 4KD4 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT TITLE 2 V23L/L25V/V66I/I72V AT 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, PDTP, CAVITY, PRESSURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,E.FLORES,J.L.SCHLESSMAN,A.HEROUX,B.GARCIA-MORENO E. REVDAT 2 20-SEP-23 4KD4 1 REMARK SEQADV LINK REVDAT 1 08-MAY-13 4KD4 0 JRNL AUTH J.A.CARO,J.L.SCHLESSMAN,B.GARCIA-MORENO E. JRNL TITL PRESSURE EFFECTS IN PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20389 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) : 0.177 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1045 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1389 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1060 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.18000 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.754 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1190 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1624 ; 1.996 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 154 ; 6.488 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;33.537 ;24.898 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 238 ;16.466 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;11.884 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 182 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 854 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 30 REMARK 3 ORIGIN FOR THE GROUP (A): -9.9508 -3.2069 0.2608 REMARK 3 T TENSOR REMARK 3 T11: 0.1427 T22: 0.1678 REMARK 3 T33: 0.0817 T12: -0.0085 REMARK 3 T13: -0.0233 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 3.2377 L22: 3.5153 REMARK 3 L33: 3.1972 L12: -0.5857 REMARK 3 L13: -0.4860 L23: -0.7386 REMARK 3 S TENSOR REMARK 3 S11: 0.2607 S12: 0.0336 S13: -0.1676 REMARK 3 S21: -0.1564 S22: -0.1267 S23: -0.2099 REMARK 3 S31: 0.0715 S32: 0.2448 S33: -0.1341 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 31 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): -16.1463 9.1094 3.9462 REMARK 3 T TENSOR REMARK 3 T11: 0.3018 T22: 0.1021 REMARK 3 T33: 0.1172 T12: -0.0219 REMARK 3 T13: 0.1045 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 3.4050 L22: 0.6819 REMARK 3 L33: 4.3792 L12: 0.3099 REMARK 3 L13: -2.5668 L23: -0.8395 REMARK 3 S TENSOR REMARK 3 S11: 0.5848 S12: -0.1325 S13: 0.4171 REMARK 3 S21: 0.0534 S22: -0.0460 S23: -0.0075 REMARK 3 S31: -0.9520 S32: 0.0527 S33: -0.5388 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 63 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): -15.5406 -3.3421 1.2166 REMARK 3 T TENSOR REMARK 3 T11: 0.1029 T22: 0.1387 REMARK 3 T33: 0.0893 T12: -0.0144 REMARK 3 T13: -0.0317 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 1.8225 L22: 1.3646 REMARK 3 L33: 4.0882 L12: -0.0249 REMARK 3 L13: -0.4253 L23: -0.1221 REMARK 3 S TENSOR REMARK 3 S11: 0.0502 S12: -0.0717 S13: -0.0999 REMARK 3 S21: -0.0441 S22: 0.0291 S23: -0.0012 REMARK 3 S31: -0.0499 S32: 0.0899 S33: -0.0793 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 98 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): -28.3017 3.5182 5.8652 REMARK 3 T TENSOR REMARK 3 T11: 0.1179 T22: 0.2526 REMARK 3 T33: 0.0623 T12: 0.0841 REMARK 3 T13: 0.0172 T23: 0.0553 REMARK 3 L TENSOR REMARK 3 L11: 1.7215 L22: 1.2920 REMARK 3 L33: 6.2642 L12: -0.4548 REMARK 3 L13: -1.1300 L23: 0.8087 REMARK 3 S TENSOR REMARK 3 S11: 0.2434 S12: 0.1601 S13: -0.0339 REMARK 3 S21: -0.0498 S22: -0.0723 S23: 0.2124 REMARK 3 S31: -0.6137 S32: -0.9357 S33: -0.1711 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4KD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-11 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) : 0.9790 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) WITH REMARK 200 CRYOGENICALLY-COOLED FIRST REMARK 200 CRYSTAL AND SAGITTALLY-BENT REMARK 200 SECOND CRYSTAL HORIZONTALLY- REMARK 200 FOCUSING AT 3.3:1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20413 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 : 12.60 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRY 1SNC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% 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 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.40300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.70150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.10450 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 LYS A 48 REMARK 465 LYS A 49 REMARK 465 GLY A 50 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 -155.09 -154.88 REMARK 500 LYS A 45 -70.32 -100.82 REMARK 500 TYR A 54 -6.27 72.65 REMARK 500 ASN A 138 -104.34 54.17 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 ASP A 40 OD1 93.2 REMARK 620 3 THR A 41 O 93.3 84.3 REMARK 620 4 THP A 202 O6P 102.6 72.8 152.6 REMARK 620 5 HOH A 331 O 81.8 143.9 60.6 143.2 REMARK 620 6 HOH A 368 O 165.5 87.2 72.2 91.4 89.4 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SNC RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL REMARK 900 NUCLEASE, CA2+, AND THE INHIBITOR PDTP, REFINED AT 1.65 ANGSTROMS DBREF 4KD4 A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 4KD4 LEU A 23 UNP P00644 VAL 105 ENGINEERED MUTATION SEQADV 4KD4 VAL A 25 UNP P00644 LEU 107 ENGINEERED MUTATION SEQADV 4KD4 ILE A 66 UNP P00644 VAL 148 ENGINEERED MUTATION SEQADV 4KD4 VAL A 72 UNP P00644 ILE 154 ENGINEERED MUTATION SEQRES 1 A 149 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 A 149 LEU ILE LYS ALA ILE ASP GLY ASP THR LEU LYS VAL MET SEQRES 3 A 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 149 ASP THR PRO GLU THR LYS HIS PRO LYS LYS GLY VAL GLU SEQRES 5 A 149 LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS MET SEQRES 6 A 149 ILE GLU ASN ALA LYS LYS VAL GLU VAL GLU PHE ASP LYS SEQRES 7 A 149 GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA TYR SEQRES 8 A 149 ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU VAL SEQRES 9 A 149 ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS PRO SEQRES 10 A 149 ASN ASN THR HIS GLU GLN HIS LEU ARG LYS SER GLU ALA SEQRES 11 A 149 GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER GLU ASP SEQRES 12 A 149 ASN ALA ASP SER GLY GLN HET CA A 201 1 HET THP A 202 25 HET MRD A 203 8 HET PO4 A 204 5 HETNAM CA CALCIUM ION HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM PO4 PHOSPHATE ION FORMUL 2 CA CA 2+ FORMUL 3 THP C10 H16 N2 O11 P2 FORMUL 4 MRD C6 H14 O2 FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *96(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 VAL A 72 PHE A 76 -1 N GLU A 73 O TYR A 93 SHEET 4 A 7 GLU A 10 ALA A 17 -1 N GLU A 10 O VAL 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 LEU 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 OD1 ASP A 21 CA CA A 201 1555 1555 2.47 LINK OD1 ASP A 40 CA CA A 201 1555 1555 2.29 LINK O THR A 41 CA CA A 201 1555 1555 2.74 LINK CA CA A 201 O6P THP A 202 1555 1555 2.96 LINK CA CA A 201 O HOH A 331 1555 1555 2.78 LINK CA CA A 201 O HOH A 368 1555 1555 2.43 CISPEP 1 LYS A 116 PRO A 117 0 6.14 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 THP A 202 SITE 2 AC1 7 HOH A 328 HOH A 331 HOH A 368 SITE 1 AC2 17 ARG A 35 ASP A 40 LYS A 71 LYS A 84 SITE 2 AC2 17 TYR A 85 ARG A 87 LEU A 89 TYR A 113 SITE 3 AC2 17 TYR A 115 CA A 201 HOH A 310 HOH A 317 SITE 4 AC2 17 HOH A 319 HOH A 328 HOH A 339 HOH A 355 SITE 5 AC2 17 HOH A 362 SITE 1 AC3 4 PHE A 61 LYS A 116 HOH A 364 HOH A 395 SITE 1 AC4 3 MET A 32 THR A 82 HOH A 381 CRYST1 47.640 47.640 62.806 90.00 90.00 90.00 P 41 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 0.020991 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015922 0.00000