HEADER HYDROLASE 10-FEB-11 3QON OBSLTE 06-SEP-17 3QON 6AMF TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS/V23K/L36E TITLE 2 AT PH 7 DETERMINED AT 100 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DELETION UNP RESIDUES 126-131; COMPND 5 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE, COMPND 6 NUCLEASE B, NUCLEASE A; COMPND 7 EC: 3.1.31.1; COMPND 8 ENGINEERED: YES; COMPND 9 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, ION PAIR, HYPERSTABLE, PDTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ROBINSON,J.L.SCHLESSMAN,E.B.GARCIA-MORENO REVDAT 2 06-SEP-17 3QON 1 OBSLTE REVDAT 1 16-MAR-11 3QON 0 JRNL AUTH E.B.GARCIA-MORENOE,A.ROBINSON,J.L.SCHLESSMAN,A.HEROUX JRNL TITL REVERSAL OF AN INTERNAL ION PAIR IN THE HYDROPHOBIC INTERIOR JRNL TITL 2 OF STAPHYLOCOCCAL NUCLEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 9083 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 454 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 650 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1036 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 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): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.871 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1080 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1451 ; 1.664 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 128 ; 6.697 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;33.935 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 211 ;16.208 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 7.333 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 153 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 785 ; 0.011 ; 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): 639 ; 1.258 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 2.134 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 441 ; 3.497 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 431 ; 5.234 ; 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 26 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0480 -3.8730 4.0410 REMARK 3 T TENSOR REMARK 3 T11: 0.0702 T22: 0.0634 REMARK 3 T33: 0.0544 T12: 0.0351 REMARK 3 T13: -0.0080 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.9274 L22: 2.4437 REMARK 3 L33: 0.0827 L12: -0.1224 REMARK 3 L13: 0.2636 L23: 0.5557 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: -0.0501 S13: -0.1056 REMARK 3 S21: 0.1129 S22: 0.0251 S23: -0.0874 REMARK 3 S31: 0.0698 S32: 0.0097 S33: 0.0188 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 27 A 36 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6660 -3.5870 -0.0400 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.0840 REMARK 3 T33: 0.0509 T12: 0.0082 REMARK 3 T13: -0.0083 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.9061 L22: 3.5698 REMARK 3 L33: 0.1479 L12: -0.8301 REMARK 3 L13: -0.2732 L23: 1.7313 REMARK 3 S TENSOR REMARK 3 S11: -0.0149 S12: 0.0289 S13: 0.0896 REMARK 3 S21: -0.1975 S22: 0.2239 S23: -0.3029 REMARK 3 S31: -0.0747 S32: 0.0512 S33: -0.2090 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 80 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1460 2.9250 9.0040 REMARK 3 T TENSOR REMARK 3 T11: 0.0686 T22: 0.0851 REMARK 3 T33: -0.0044 T12: 0.0119 REMARK 3 T13: -0.0089 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.2804 L22: 1.9364 REMARK 3 L33: 0.6601 L12: -0.5860 REMARK 3 L13: 0.0848 L23: 0.3348 REMARK 3 S TENSOR REMARK 3 S11: -0.1156 S12: -0.1523 S13: -0.0609 REMARK 3 S21: 0.1588 S22: 0.1366 S23: -0.0018 REMARK 3 S31: 0.0082 S32: 0.0155 S33: -0.0210 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 97 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0870 1.7200 0.0300 REMARK 3 T TENSOR REMARK 3 T11: 0.0699 T22: 0.0541 REMARK 3 T33: 0.0574 T12: -0.0297 REMARK 3 T13: 0.0217 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 2.7817 L22: 1.9877 REMARK 3 L33: -0.3141 L12: 0.4436 REMARK 3 L13: -0.2107 L23: -0.6038 REMARK 3 S TENSOR REMARK 3 S11: -0.0935 S12: 0.1558 S13: -0.1280 REMARK 3 S21: -0.0228 S22: 0.0674 S23: -0.0248 REMARK 3 S31: 0.0448 S32: -0.0135 S33: 0.0261 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 98 A 130 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5240 10.2360 3.1220 REMARK 3 T TENSOR REMARK 3 T11: 0.0474 T22: 0.0581 REMARK 3 T33: 0.0780 T12: 0.0000 REMARK 3 T13: -0.0129 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 1.8790 L22: 1.8044 REMARK 3 L33: -0.1135 L12: -0.8678 REMARK 3 L13: -0.3672 L23: 0.6935 REMARK 3 S TENSOR REMARK 3 S11: -0.0337 S12: 0.0642 S13: 0.1050 REMARK 3 S21: 0.0156 S22: 0.0146 S23: 0.2329 REMARK 3 S31: 0.0119 S32: 0.0270 S33: 0.0192 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 131 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5850 15.6680 15.0630 REMARK 3 T TENSOR REMARK 3 T11: 0.0566 T22: 0.0309 REMARK 3 T33: 0.1628 T12: 0.0460 REMARK 3 T13: 0.1436 T23: -0.0752 REMARK 3 L TENSOR REMARK 3 L11: 10.7288 L22: 3.0852 REMARK 3 L33: 7.5853 L12: 3.4775 REMARK 3 L13: 4.3164 L23: 0.3525 REMARK 3 S TENSOR REMARK 3 S11: -0.1807 S12: -0.0706 S13: 1.0781 REMARK 3 S21: 0.6698 S22: -0.1286 S23: 0.9054 REMARK 3 S31: 0.0288 S32: 0.1149 S33: 0.3094 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 3QON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000063908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GE111 REMARK 200 OPTICS : MULTI-LAYER OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT, XPREP REMARK 200 DATA SCALING SOFTWARE : XPREP REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.77 REMARK 200 R MERGE (I) : 0.06530 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.26 REMARK 200 R MERGE FOR SHELL (I) : 0.27740 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 PDTP, CACL2, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 30.13150 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 ILE A 18 -74.52 -122.09 REMARK 500 LYS A 28 39.41 39.92 REMARK 500 TYR A 54 -0.02 74.78 REMARK 500 ASP A 77 -159.59 -90.99 REMARK 500 ASN A 138 -109.00 48.46 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 HOH A 175 O REMARK 620 2 ASP A 40 OD1 140.3 REMARK 620 3 HOH A 171 O 73.3 134.0 REMARK 620 4 THR A 41 O 67.8 76.3 139.3 REMARK 620 5 GLU A 43 OE2 79.2 128.2 77.8 105.5 REMARK 620 6 ASP A 21 OD2 80.2 80.9 75.6 86.3 150.1 REMARK 620 7 THP A 151 O5P 150.5 65.3 77.3 141.1 93.5 93.9 REMARK 620 8 HOH A 254 O 110.4 56.0 159.4 53.8 82.9 124.8 96.8 REMARK 620 N 1 2 3 4 5 6 7 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 STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS REMARK 900 RELATED ID: 3NHH RELATED DB: PDB REMARK 900 STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS/V23E/L36K REMARK 900 RELATED ID: 3QOJ RELATED DB: PDB REMARK 900 STAPHYLOCOCCAL NUCLEASE VARIANT D+PHS/V23K DBREF 3QON A 1 149 UNP P00644 NUC_STAAU 41 189 SEQADV 3QON LYS A 23 UNP P00644 VAL 63 ENGINEERED MUTATION SEQADV 3QON GLU A 36 UNP P00644 LEU 76 ENGINEERED MUTATION SEQADV 3QON A UNP P00644 THR 84 DELETION SEQADV 3QON A UNP P00644 LYS 85 DELETION SEQADV 3QON A UNP P00644 HIS 86 DELETION SEQADV 3QON A UNP P00644 PRO 87 DELETION SEQADV 3QON A UNP P00644 LYS 88 DELETION SEQADV 3QON A UNP P00644 LYS 89 DELETION SEQADV 3QON PHE A 50 UNP P00644 GLY 90 ENGINEERED MUTATION SEQADV 3QON ASN A 51 UNP P00644 VAL 91 ENGINEERED MUTATION SEQADV 3QON GLY A 117 UNP P00644 PRO 157 ENGINEERED MUTATION SEQADV 3QON LEU A 124 UNP P00644 HIS 164 ENGINEERED MUTATION SEQADV 3QON ALA A 128 UNP P00644 SER 168 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 GLU 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 *95(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 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 LYS A 24 N LYS A 16 SHEET 6 A 7 GLN A 30 GLU 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 THR A 33 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 CA CA A 150 O HOH A 175 1555 1555 2.75 LINK OD1 ASP A 40 CA CA A 150 1555 1555 2.83 LINK CA CA A 150 O HOH A 171 1555 1555 2.84 LINK O THR A 41 CA CA A 150 1555 1555 2.87 LINK OE2 GLU A 43 CA CA A 150 1555 1555 2.95 LINK OD2 ASP A 21 CA CA A 150 1555 1555 3.02 LINK CA CA A 150 O5P THP A 151 1555 1555 3.18 LINK CA CA A 150 O HOH A 254 1555 1555 3.19 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC1 7 THP A 151 HOH A 171 HOH A 175 SITE 1 AC2 19 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC2 19 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC2 19 LYS A 127 CA A 150 HOH A 158 HOH A 171 SITE 4 AC2 19 HOH A 176 HOH A 188 HOH A 203 HOH A 209 SITE 5 AC2 19 HOH A 213 HOH A 249 HOH A 262 CRYST1 31.137 60.263 38.288 90.00 94.33 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 0.032116 0.000000 0.002430 0.00000 SCALE2 0.000000 0.016594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026192 0.00000