HEADER HYDROLASE 09-NOV-05 2EY5 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE MUTANT T41S COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAPHYLOCOCCAL NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THERMONUCLEASE; TNASE; MICROCOCCAL NUCLEASE; 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 GENE: NUC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: AR120; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PL13 KEYWDS DNA HYDROLASE; RNA HYDROLASE; ENDONUCLEASE; CALCIUM; SIGNAL, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Z.LU,J.SAKON,W.E.STITES REVDAT 6 14-FEB-24 2EY5 1 REMARK REVDAT 5 20-OCT-21 2EY5 1 SEQADV REVDAT 4 24-JUL-19 2EY5 1 REMARK REVDAT 3 18-OCT-17 2EY5 1 REMARK REVDAT 2 24-FEB-09 2EY5 1 VERSN REVDAT 1 24-OCT-06 2EY5 0 JRNL AUTH J.Z.LU,J.SAKON,W.E.STITES JRNL TITL THREONINE MUTANTS 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 : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.195 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.194 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 466 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9242 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.161 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.160 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 356 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1081 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1126.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4516 REMARK 3 NUMBER OF RESTRAINTS : 4409 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.022 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.031 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.034 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.156 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9242 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM PHOSPHATE BUFFER, 45% MPD, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, 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 31.85650 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 15.92825 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 47.78475 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 LYS A 49 C - N - CA ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG A 81 CD - NE - CZ ANGL. DEV. = 12.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 46 120.91 77.91 REMARK 500 LYS A 49 -96.81 155.69 REMARK 500 VAL A 51 74.93 -111.69 REMARK 500 TYR A 54 -8.22 81.36 REMARK 500 ASN A 119 19.25 -152.62 REMARK 500 ASN A 138 -104.91 37.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EY0 RELATED DB: PDB REMARK 900 WT REMARK 900 RELATED ID: 2EXZ RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EY1 RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EY2 RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EY6 RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYF RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYH RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYJ RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYL RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYM RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYO RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2EYP RELATED DB: PDB REMARK 900 THR MUTANT REMARK 900 RELATED ID: 2F0D RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0E RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0F RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0G RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0H RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0I RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0J RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0K RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0L RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0M RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0N RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0O RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0P RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0Q RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0S RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0T RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0U RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0V RELATED DB: PDB REMARK 900 PACKING MUTANT REMARK 900 RELATED ID: 2F0W RELATED DB: PDB REMARK 900 PACKING MUTANT DBREF 2EY5 A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 2EY5 SER A 41 UNP P00644 THR 120 ENGINEERED MUTATION SEQADV 2EY5 HIS A 124 UNP P00644 LEU 203 VARIANT 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 VAL LYS LEU MET SEQRES 3 A 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 149 ASP SER 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 VAL GLU ASN ALA LYS LYS ILE 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 FORMUL 2 HOH *45(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 ILE A 72 PHE A 76 -1 N GLU A 75 O TYR A 91 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 CISPEP 1 LYS A 116 PRO A 117 0 3.46 CRYST1 48.149 48.149 63.713 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 0.020769 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020769 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015695 0.00000