HEADER HYDROLASE 16-MAR-11 3R3O TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS T62A AT TITLE 2 CRYOGENIC TEMPERATURE AND WITH HIGH REDUNDANCY 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 HYPERSTABLE VARIANT, PDTP, PRESSURE, CAVITY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,J.L.SCHLESSMAN,B.GARCIA-MORENO E. REVDAT 3 13-SEP-23 3R3O 1 REMARK SEQADV LINK REVDAT 2 23-MAY-12 3R3O 1 JRNL VERSN REVDAT 1 30-MAR-11 3R3O 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11067 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1092 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 752 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2350 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 : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.52000 REMARK 3 B22 (A**2) : -1.25000 REMARK 3 B33 (A**2) : 2.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.843 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1109 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1505 ; 1.338 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 140 ; 6.582 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;32.516 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 211 ;17.797 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 6.490 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 163 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 819 ; 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): 657 ; 1.046 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1057 ; 1.688 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 452 ; 2.993 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 442 ; 4.399 ; 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): 12.7226 -18.3325 3.0994 REMARK 3 T TENSOR REMARK 3 T11: 0.0886 T22: 0.0720 REMARK 3 T33: 0.1126 T12: 0.0132 REMARK 3 T13: -0.0032 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.2854 L22: 3.0529 REMARK 3 L33: 0.5043 L12: -0.4599 REMARK 3 L13: -0.3761 L23: 0.7873 REMARK 3 S TENSOR REMARK 3 S11: -0.0977 S12: 0.0670 S13: -0.1990 REMARK 3 S21: 0.0202 S22: 0.0942 S23: -0.0327 REMARK 3 S31: -0.0161 S32: 0.0833 S33: 0.0035 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): 16.6349 -16.7285 0.8088 REMARK 3 T TENSOR REMARK 3 T11: 0.0543 T22: 0.0709 REMARK 3 T33: 0.2200 T12: 0.0206 REMARK 3 T13: 0.0262 T23: -0.0540 REMARK 3 L TENSOR REMARK 3 L11: 0.8620 L22: 4.2963 REMARK 3 L33: 0.3868 L12: -1.9207 REMARK 3 L13: 0.5772 L23: -1.2850 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: 0.0048 S13: 0.0637 REMARK 3 S21: -0.0977 S22: -0.0168 S23: -0.1963 REMARK 3 S31: 0.0287 S32: 0.0042 S33: 0.0063 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 74 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3228 -10.7659 8.9884 REMARK 3 T TENSOR REMARK 3 T11: 0.1055 T22: 0.1479 REMARK 3 T33: 0.1016 T12: 0.0145 REMARK 3 T13: -0.0139 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 2.7479 L22: 2.4397 REMARK 3 L33: 1.0432 L12: -0.2991 REMARK 3 L13: -0.3144 L23: 0.1901 REMARK 3 S TENSOR REMARK 3 S11: -0.0668 S12: -0.3348 S13: -0.0310 REMARK 3 S21: 0.2616 S22: 0.0573 S23: -0.0694 REMARK 3 S31: 0.0381 S32: 0.0437 S33: 0.0096 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 75 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8752 -7.4806 1.3604 REMARK 3 T TENSOR REMARK 3 T11: 0.0650 T22: 0.0613 REMARK 3 T33: 0.0634 T12: -0.0004 REMARK 3 T13: 0.0046 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 2.3411 L22: 1.9993 REMARK 3 L33: 1.0252 L12: -0.2994 REMARK 3 L13: 0.1586 L23: 0.2413 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: 0.0685 S13: 0.0071 REMARK 3 S21: -0.0843 S22: 0.0331 S23: 0.0669 REMARK 3 S31: -0.0241 S32: -0.0232 S33: -0.0336 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): -0.7162 0.5941 11.0248 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 0.1113 REMARK 3 T33: 0.1337 T12: 0.0354 REMARK 3 T13: 0.0372 T23: -0.0566 REMARK 3 L TENSOR REMARK 3 L11: 2.9365 L22: 2.7752 REMARK 3 L33: 4.9458 L12: -1.0172 REMARK 3 L13: 1.7216 L23: 0.4687 REMARK 3 S TENSOR REMARK 3 S11: -0.2575 S12: -0.5276 S13: 0.3035 REMARK 3 S21: 0.3602 S22: 0.1235 S23: 0.2920 REMARK 3 S31: -0.2422 S32: -0.2043 S33: 0.1340 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 3R3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064448. 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) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GE111 REMARK 200 OPTICS : MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : APEX REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11067 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 : 11.42 REMARK 200 R MERGE (I) : 0.03330 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26580 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.340 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 (%): 44.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% 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 30.30600 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 70 CD CE NZ REMARK 480 LYS A 97 CD CE NZ 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 -74.66 -117.85 REMARK 500 ASP A 19 -159.81 -144.84 REMARK 500 TYR A 54 -1.81 73.76 REMARK 500 ASN A 138 -104.25 51.05 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 80.3 REMARK 620 3 THR A 41 O 89.7 74.0 REMARK 620 4 GLU A 43 OE2 154.6 123.6 104.6 REMARK 620 5 HOH A 158 O 76.1 135.1 142.2 79.9 REMARK 620 6 HOH A 159 O 83.0 136.6 66.2 83.7 77.3 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 VARIANT DELTA+PHS REMARK 900 RELATED ID: 3MXP RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT DELTA+PHS T62A REMARK 900 RELATED ID: 3MEH RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT DELTA+PHS I92A REMARK 900 RELATED ID: 3MHB RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT DELTA+PHS L38A REMARK 900 RELATED ID: 3MZ5 RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT DELTA+PHS L103A REMARK 900 RELATED ID: 3MVV RELATED DB: PDB REMARK 900 STAPH NUCLEASE VARIANT DELTA+PHS F34A DBREF 3R3O A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3R3O A UNP P00644 THR 126 DELETION SEQADV 3R3O A UNP P00644 LYS 127 DELETION SEQADV 3R3O A UNP P00644 HIS 128 DELETION SEQADV 3R3O A UNP P00644 PRO 129 DELETION SEQADV 3R3O A UNP P00644 LYS 130 DELETION SEQADV 3R3O A UNP P00644 LYS 131 DELETION SEQADV 3R3O PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3R3O ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3R3O ALA A 62 UNP P00644 THR 144 ENGINEERED MUTATION SEQADV 3R3O GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3R3O LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3R3O 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 ALA 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 *96(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 LYS A 9 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 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 150 1555 1555 2.83 LINK OD1 ASP A 40 CA CA A 150 1555 1555 2.74 LINK O THR A 41 CA CA A 150 1555 1555 2.87 LINK OE2 GLU A 43 CA CA A 150 1555 1555 2.99 LINK CA CA A 150 O HOH A 158 1555 1555 2.83 LINK CA CA A 150 O HOH A 159 1555 1555 2.84 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 158 HOH A 159 SITE 1 AC2 20 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC2 20 ARG A 87 TYR A 113 TYR A 115 LYS A 127 SITE 3 AC2 20 CA A 150 HOH A 153 HOH A 158 HOH A 160 SITE 4 AC2 20 HOH A 173 HOH A 187 HOH A 196 HOH A 204 SITE 5 AC2 20 HOH A 209 HOH A 220 HOH A 236 HOH A 247 CRYST1 31.132 60.612 37.632 90.00 94.04 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 0.032121 0.000000 0.002269 0.00000 SCALE2 0.000000 0.016498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026639 0.00000