HEADER HYDROLASE 23-JAN-12 4DFA TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS TITLE 2 I92A/L36A 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, HYPERSTABLE VARIANT, PDTP, CAVITY, PRESSURE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,I.A.CLARK,J.L.SCHLESSMAN,A.HEROUX,B.GARCIA-MORENO E. REVDAT 2 13-SEP-23 4DFA 1 REMARK SEQADV LINK REVDAT 1 01-FEB-12 4DFA 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 27001 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1356 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1487 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1027 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.89000 REMARK 3 B22 (A**2) : -1.56000 REMARK 3 B33 (A**2) : 2.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.74000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.973 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1153 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1569 ; 1.942 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 153 ; 6.340 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;33.619 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 234 ;15.943 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 8.241 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 171 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 843 ; 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): 677 ; 1.390 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1098 ; 2.175 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 476 ; 3.364 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 458 ; 4.969 ; 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 12 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9186 -80.8026 -4.2637 REMARK 3 T TENSOR REMARK 3 T11: 0.0823 T22: 0.0876 REMARK 3 T33: 0.3564 T12: -0.0084 REMARK 3 T13: -0.0214 T23: -0.0856 REMARK 3 L TENSOR REMARK 3 L11: 4.1500 L22: 9.4507 REMARK 3 L33: 5.3649 L12: -1.3986 REMARK 3 L13: 0.8135 L23: -4.3051 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: 0.5045 S13: -0.9335 REMARK 3 S21: -0.4650 S22: 0.0952 S23: 0.6616 REMARK 3 S31: 0.0484 S32: -0.1117 S33: -0.0761 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 13 A 34 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8716 -79.0942 4.7100 REMARK 3 T TENSOR REMARK 3 T11: 0.1252 T22: 0.1129 REMARK 3 T33: 0.1809 T12: 0.0262 REMARK 3 T13: 0.0001 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.9064 L22: 3.5464 REMARK 3 L33: 0.9840 L12: -1.0488 REMARK 3 L13: -0.6951 L23: 1.5863 REMARK 3 S TENSOR REMARK 3 S11: -0.1031 S12: -0.1182 S13: -0.2688 REMARK 3 S21: 0.1648 S22: 0.1214 S23: -0.2030 REMARK 3 S31: 0.0820 S32: 0.0945 S33: -0.0183 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 35 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4008 -71.6864 8.6771 REMARK 3 T TENSOR REMARK 3 T11: 0.1561 T22: 0.1544 REMARK 3 T33: 0.1219 T12: 0.0139 REMARK 3 T13: 0.0100 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 3.2263 L22: 3.2422 REMARK 3 L33: 1.0821 L12: -0.2604 REMARK 3 L13: -0.2762 L23: 0.4145 REMARK 3 S TENSOR REMARK 3 S11: -0.0831 S12: -0.3298 S13: -0.0906 REMARK 3 S21: 0.3625 S22: 0.0446 S23: 0.0292 REMARK 3 S31: 0.1391 S32: 0.0617 S33: 0.0385 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): 12.3632 -72.9085 -0.1784 REMARK 3 T TENSOR REMARK 3 T11: 0.1269 T22: 0.1280 REMARK 3 T33: 0.1392 T12: 0.0018 REMARK 3 T13: 0.0043 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 4.3190 L22: 3.1577 REMARK 3 L33: 0.7041 L12: 0.1474 REMARK 3 L13: -0.4811 L23: 0.1334 REMARK 3 S TENSOR REMARK 3 S11: -0.0837 S12: 0.2258 S13: -0.2124 REMARK 3 S21: -0.0500 S22: 0.0442 S23: -0.0753 REMARK 3 S31: 0.0603 S32: 0.0036 S33: 0.0395 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): 3.5937 -64.4268 3.0292 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.1055 REMARK 3 T33: 0.1715 T12: 0.0039 REMARK 3 T13: 0.0015 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 3.1182 L22: 2.6743 REMARK 3 L33: 0.7634 L12: -0.4050 REMARK 3 L13: -0.1388 L23: 0.5144 REMARK 3 S TENSOR REMARK 3 S11: -0.0585 S12: 0.0598 S13: 0.1911 REMARK 3 S21: -0.0167 S22: 0.0198 S23: 0.2110 REMARK 3 S31: 0.0075 S32: -0.0583 S33: 0.0387 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): -0.5120 -59.1052 14.6159 REMARK 3 T TENSOR REMARK 3 T11: 0.1715 T22: 0.1819 REMARK 3 T33: 0.1934 T12: 0.0481 REMARK 3 T13: 0.0685 T23: -0.1049 REMARK 3 L TENSOR REMARK 3 L11: 11.5628 L22: 3.8904 REMARK 3 L33: 6.4249 L12: -0.1169 REMARK 3 L13: 6.1271 L23: -1.1031 REMARK 3 S TENSOR REMARK 3 S11: -0.2874 S12: -0.7494 S13: 0.7013 REMARK 3 S21: 0.5771 S22: 0.1544 S23: 0.4429 REMARK 3 S31: -0.2160 S32: -0.3146 S33: 0.1330 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 4DFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070256. 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 : 7.0 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 : SI(111) REMARK 200 OPTICS : NULL 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 : 27015 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.404 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 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 (%): 45.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 7.0, 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 30.22300 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 ASN A 138 -106.83 56.72 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 OD2 REMARK 620 2 ASP A 40 OD1 81.7 REMARK 620 3 THR A 41 O 88.2 78.2 REMARK 620 4 GLU A 43 OE2 152.9 124.3 103.1 REMARK 620 5 THP A 202 O5P 93.5 68.2 145.7 90.7 REMARK 620 6 HOH A 345 O 74.8 135.0 137.4 80.4 75.4 REMARK 620 7 HOH A 348 O 81.5 139.6 64.8 81.3 149.3 74.1 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS AT REMARK 900 CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3MEH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS I92A REMARK 900 AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3NP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS L36A REMARK 900 AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3VA5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS I92A/ REMARK 900 V23A AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3V2T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS I92A/ REMARK 900 V66A AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3SXH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS I92A/ REMARK 900 L103A AT CRYOGENIC TEMPERATURE DBREF 4DFA A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 4DFA ALA A 36 UNP P00644 LEU 118 ENGINEERED MUTATION SEQADV 4DFA A UNP P00644 THR 126 DELETION SEQADV 4DFA A UNP P00644 LYS 127 DELETION SEQADV 4DFA A UNP P00644 HIS 128 DELETION SEQADV 4DFA A UNP P00644 PRO 129 DELETION SEQADV 4DFA A UNP P00644 LYS 130 DELETION SEQADV 4DFA A UNP P00644 LYS 131 DELETION SEQADV 4DFA PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 4DFA ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 4DFA ALA A 92 UNP P00644 ILE 174 ENGINEERED MUTATION SEQADV 4DFA GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 4DFA LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 4DFA 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 ALA 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 ALA 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 201 1 HET THP A 202 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 *130(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 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 ALA 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 201 1555 1555 2.88 LINK OD1 ASP A 40 CA CA A 201 1555 1555 2.71 LINK O THR A 41 CA CA A 201 1555 1555 2.80 LINK OE2 GLU A 43 CA CA A 201 1555 1555 2.99 LINK CA CA A 201 O5P THP A 202 1555 1555 3.14 LINK CA CA A 201 O HOH A 345 1555 1555 2.81 LINK CA CA A 201 O HOH A 348 1555 1555 2.90 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC1 7 THP A 202 HOH A 345 HOH A 348 SITE 1 AC2 23 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC2 23 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC2 23 LYS A 127 CA A 201 HOH A 301 HOH A 305 SITE 4 AC2 23 HOH A 307 HOH A 314 HOH A 345 HOH A 346 SITE 5 AC2 23 HOH A 347 HOH A 353 HOH A 356 HOH A 358 SITE 6 AC2 23 HOH A 359 HOH A 360 HOH A 361 CRYST1 31.113 60.446 38.309 90.00 93.81 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 0.032141 0.000000 0.002139 0.00000 SCALE2 0.000000 0.016544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026161 0.00000