HEADER HYDROLASE 28-JUN-10 3NP8 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS L36A AT TITLE 2 CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DELETION UNP RESIDUES 126-131; COMPND 5 EC: 3.1.31.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 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,E.B.GARCIA-MORENO,A.HEROUX REVDAT 3 06-SEP-23 3NP8 1 REMARK SEQADV LINK REVDAT 2 23-MAY-12 3NP8 1 JRNL VERSN REVDAT 1 29-JUN-11 3NP8 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 15410 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 963 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.50000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 2.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.70000 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): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.646 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1095 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1482 ; 1.677 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 6.589 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 47 ;31.862 ;24.894 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 211 ;18.194 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 6.858 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 162 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 797 ; 0.014 ; 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): 651 ; 1.353 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1048 ; 1.977 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 444 ; 3.332 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 430 ; 4.430 ; 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 42 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6308 -1.5349 3.1046 REMARK 3 T TENSOR REMARK 3 T11: 0.1329 T22: 0.0604 REMARK 3 T33: 0.1411 T12: 0.0190 REMARK 3 T13: -0.0017 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.6820 L22: 4.7954 REMARK 3 L33: -0.0258 L12: -1.2673 REMARK 3 L13: -0.5952 L23: 0.9327 REMARK 3 S TENSOR REMARK 3 S11: -0.1585 S12: 0.0654 S13: -0.4283 REMARK 3 S21: -0.0294 S22: 0.1445 S23: 0.0028 REMARK 3 S31: 0.1857 S32: 0.1028 S33: 0.0140 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 43 A 65 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9008 2.9859 15.3161 REMARK 3 T TENSOR REMARK 3 T11: 0.2273 T22: 0.2690 REMARK 3 T33: -0.0026 T12: 0.0741 REMARK 3 T13: 0.0218 T23: 0.0642 REMARK 3 L TENSOR REMARK 3 L11: 7.8346 L22: 10.9450 REMARK 3 L33: 2.4774 L12: 1.4440 REMARK 3 L13: 0.4146 L23: 3.4270 REMARK 3 S TENSOR REMARK 3 S11: -0.3484 S12: -1.2066 S13: -0.0670 REMARK 3 S21: 0.5229 S22: 0.3244 S23: 0.1988 REMARK 3 S31: 0.2745 S32: 0.1946 S33: 0.0239 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 66 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8962 2.3199 0.6515 REMARK 3 T TENSOR REMARK 3 T11: 0.0995 T22: 0.0967 REMARK 3 T33: 0.1144 T12: -0.0420 REMARK 3 T13: -0.0293 T23: 0.0239 REMARK 3 L TENSOR REMARK 3 L11: 5.6571 L22: 3.5725 REMARK 3 L33: 1.1968 L12: -0.4013 REMARK 3 L13: 0.2591 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: -0.0852 S12: 0.5140 S13: -0.1053 REMARK 3 S21: -0.1633 S22: 0.1490 S23: 0.2984 REMARK 3 S31: 0.2507 S32: 0.0166 S33: -0.0639 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 100 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5604 11.6490 0.5354 REMARK 3 T TENSOR REMARK 3 T11: 0.0230 T22: 0.0746 REMARK 3 T33: 0.2044 T12: -0.0399 REMARK 3 T13: -0.0723 T23: 0.1441 REMARK 3 L TENSOR REMARK 3 L11: 7.1015 L22: 7.4114 REMARK 3 L33: 0.9448 L12: -1.7679 REMARK 3 L13: -1.1911 L23: 0.3860 REMARK 3 S TENSOR REMARK 3 S11: 0.0243 S12: 0.6436 S13: 0.8709 REMARK 3 S21: -0.4972 S22: 0.2035 S23: 0.5227 REMARK 3 S31: -0.0866 S32: -0.0547 S33: -0.2278 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 119 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): -0.3978 15.3889 11.8884 REMARK 3 T TENSOR REMARK 3 T11: 0.0978 T22: 0.1830 REMARK 3 T33: 0.6001 T12: 0.1147 REMARK 3 T13: 0.1411 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 9.0428 L22: 3.2401 REMARK 3 L33: 5.5595 L12: 3.3171 REMARK 3 L13: 0.5942 L23: 1.7557 REMARK 3 S TENSOR REMARK 3 S11: -0.0271 S12: -0.7449 S13: 1.6865 REMARK 3 S21: 0.4691 S22: 0.3010 S23: 1.0836 REMARK 3 S31: -0.1231 S32: -0.0682 S33: -0.2739 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; U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 3NP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060107. 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 : 6.0 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 : 15463 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 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, L36A, Q30A, K64A, T82A, Y113A, REMARK 200 V114A, 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 (%): 44.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 6.0, 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 30.20200 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 ASP A 19 -154.64 -149.44 REMARK 500 TYR A 54 -2.97 70.08 REMARK 500 ASN A 118 55.25 -110.92 REMARK 500 ASN A 138 -106.14 54.04 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 81.7 REMARK 620 3 THR A 41 O 89.0 75.6 REMARK 620 4 GLU A 43 OE2 152.0 123.7 107.5 REMARK 620 5 HOH A 154 O 81.5 138.8 66.8 84.5 REMARK 620 6 HOH A 157 O 74.2 134.2 140.5 78.9 75.4 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 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 3NP8 A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3NP8 ALA A 36 UNP P00644 LEU 118 ENGINEERED MUTATION SEQADV 3NP8 A UNP P00644 THR 126 DELETION SEQADV 3NP8 A UNP P00644 LYS 127 DELETION SEQADV 3NP8 A UNP P00644 HIS 128 DELETION SEQADV 3NP8 A UNP P00644 PRO 129 DELETION SEQADV 3NP8 A UNP P00644 LYS 130 DELETION SEQADV 3NP8 A UNP P00644 LYS 131 DELETION SEQADV 3NP8 PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3NP8 ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3NP8 GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3NP8 LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3NP8 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 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 *45(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 ASP A 19 -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 151 1555 1555 2.89 LINK OD1 ASP A 40 CA CA A 151 1555 1555 2.73 LINK O THR A 41 CA CA A 151 1555 1555 2.77 LINK OE2 GLU A 43 CA CA A 151 1555 1555 3.02 LINK CA CA A 151 O HOH A 154 1555 1555 2.91 LINK CA CA A 151 O HOH A 157 1555 1555 2.82 SITE 1 AC1 19 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC1 19 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC1 19 LYS A 127 CA A 151 HOH A 153 HOH A 157 SITE 4 AC1 19 HOH A 159 HOH A 163 HOH A 165 HOH A 182 SITE 5 AC1 19 HOH A 184 HOH A 187 HOH A 190 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 154 HOH A 157 CRYST1 31.011 60.404 38.275 90.00 93.77 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 0.032247 0.000000 0.002125 0.00000 SCALE2 0.000000 0.016555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026183 0.00000