HEADER HYDROLASE 08-FEB-08 3C7Y TITLE MUTANT R96A OF T4 LYSOZYME IN WILDTYPE BACKGROUND AT 298K COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE T4; SOURCE 3 ORGANISM_COMMON: VIRUS; SOURCE 4 GENE: E; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: RR1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHS1403 KEYWDS BACTERIOPHAGE T4 LYSOZYME, VIRAL LYSOZYME, MUTATIONAL ANALYSIS, KEYWDS 2 PROTEIN ENGINEERING, THERMAL STABILITY, PROTEIN STABILITY, PROTEIN KEYWDS 3 ELECTROSTATICS, PROTEIN STRUCTURE, CATION BINDING, CHARGE BURIAL, KEYWDS 4 HYDROGEN BONDING, HELIX DIPOLE, PROTEIN CREVICES, STERIC STRAIN, KEYWDS 5 TEMPERATURE-SENSITIVE MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.H.M.MOOERS REVDAT 4 30-AUG-23 3C7Y 1 REMARK REVDAT 3 20-OCT-21 3C7Y 1 REMARK SEQADV LINK REVDAT 2 05-MAY-09 3C7Y 1 JRNL REVDAT 1 17-FEB-09 3C7Y 0 JRNL AUTH B.H.MOOERS,W.A.BAASE,J.W.WRAY,B.W.MATTHEWS JRNL TITL CONTRIBUTIONS OF ALL 20 AMINO ACIDS AT SITE 96 TO THE JRNL TITL 2 STABILITY AND STRUCTURE OF T4 LYSOZYME. JRNL REF PROTEIN SCI. V. 18 871 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19384988 JRNL DOI 10.1002/PRO.94 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.H.MOOERS,D.E.TRONRUD,B.W.MATTHEWS REMARK 1 TITL EVALUATION AT ATOMIC RESOLUTION OF THE ROLE OF STRAIN IN REMARK 1 TITL 2 DESTABILIZING THE TEMPERATURE-SENSITIVE T4 LYSOZYME MUTANT REMARK 1 TITL 3 ARG 96 --> HIS. REMARK 1 REF PROTEIN SCI. V. 18 863 2009 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 19384984 REMARK 1 DOI 10.1002/PRO.93 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 14074 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : FMUT-FWT ELECTRON DENSITY REMARK 3 MAPS REMARK 3 FREE R VALUE TEST SET SELECTION : NOT APPLICABLE REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2110 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15819 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1303 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.013 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.410 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET REMARK 3 KSOL : 0.90 REMARK 3 BSOL : 706.9 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT5G REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NATIVE K = 1.2442 OVERALL B = 0.00000 REMARK 4 REMARK 4 3C7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.7 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) : 1.5414 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAN DEIGO MULTIWIRE REMARK 200 DATA SCALING SOFTWARE : SAN DEIGO MULTIWIRE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14074 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 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: TNT REMARK 200 STARTING MODEL: 1L63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M NA/K PHOSPHATE PH 6.7 550 MM NACL REMARK 280 50 MM REDUCED BME, 50 MM OXIDIZED BME , VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.72800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.36400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.36400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.72800 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 300 REMARK: MONOMER 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 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 29 76.36 -103.73 REMARK 500 PHE A 114 49.71 -79.55 REMARK 500 ASN A 163 45.11 70.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L34 RELATED DB: PDB REMARK 900 MUTANT R96H LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 1L63 RELATED DB: PDB REMARK 900 WILDTYPE T4 LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C7W RELATED DB: PDB REMARK 900 MUTANT R96K LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C7Z RELATED DB: PDB REMARK 900 MUTANT D89A/R96H LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C80 RELATED DB: PDB REMARK 900 MUTANT R96Y LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C81 RELATED DB: PDB REMARK 900 MUTANT K85A LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C82 RELATED DB: PDB REMARK 900 MUTANT K85A/R96H LYSOZYME AT ROOM REMARK 900 RELATED ID: 3C83 RELATED DB: PDB REMARK 900 MUTANT D89A LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C8Q RELATED DB: PDB REMARK 900 MUTANT R96D LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C8R RELATED DB: PDB REMARK 900 MUTANT R96G LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3C8S RELATED DB: PDB REMARK 900 MUTANT R96E LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3CDO RELATED DB: PDB REMARK 900 MUTANT R96V LYSOZYME AT LOW TEMPERATURE REMARK 900 RELATED ID: 3CDQ RELATED DB: PDB REMARK 900 MUTANT R96S LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3CDR RELATED DB: PDB REMARK 900 MUTANT R96Q LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3CDT RELATED DB: PDB REMARK 900 MUTANT R96N LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3CDV RELATED DB: PDB REMARK 900 MUTANT R96M LYSOZYME AT ROOM TEMPERATURE REMARK 900 RELATED ID: 3F8V RELATED DB: PDB REMARK 900 R96H AT 1.08 ANG REMARK 900 RELATED ID: 3F9L RELATED DB: PDB REMARK 900 D72A AT 1.19 ANG REMARK 900 RELATED ID: 3FA0 RELATED DB: PDB REMARK 900 WILD TYPE AT 1.09 ANG REMARK 900 RELATED ID: 3FAD RELATED DB: PDB REMARK 900 D72A/R96H AT 1.20 ANG REMARK 900 RELATED ID: 3FI5 RELATED DB: PDB REMARK 900 R96W AT 1.73 ANG DBREF 3C7Y A 1 164 UNP P00720 LYS_BPT4 1 164 SEQADV 3C7Y ALA A 96 UNP P00720 ARG 96 ENGINEERED MUTATION SEQRES 1 A 164 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 164 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 164 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 164 ASN ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 164 ASN CYS ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 164 LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE SEQRES 7 A 164 LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU SEQRES 8 A 164 ASP ALA VAL ARG ALA CYS ALA LEU ILE ASN MET VAL PHE SEQRES 9 A 164 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER SEQRES 10 A 164 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 164 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 164 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 164 THR TRP ASP ALA TYR LYS ASN LEU HET CL A 168 1 HET BME A 600 4 HETNAM CL CHLORIDE ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 CL CL 1- FORMUL 3 BME C2 H6 O S FORMUL 4 HOH *54(H2 O) HELIX 1 1 ASN A 2 GLY A 12 1 11 HELIX 2 2 SER A 38 GLY A 51 1 14 HELIX 3 3 THR A 59 ASN A 81 1 23 HELIX 4 4 LYS A 83 LEU A 91 1 9 HELIX 5 5 ASP A 92 ALA A 112 1 21 HELIX 6 6 PHE A 114 GLN A 123 1 10 HELIX 7 7 ARG A 125 LYS A 135 1 11 HELIX 8 8 SER A 136 THR A 142 1 7 HELIX 9 9 THR A 142 GLY A 156 1 15 HELIX 10 10 TRP A 158 LYS A 162 5 5 SHEET 1 A 3 ARG A 14 LYS A 19 0 SHEET 2 A 3 TYR A 25 GLY A 28 -1 O THR A 26 N TYR A 18 SHEET 3 A 3 HIS A 31 THR A 34 -1 O LEU A 33 N TYR A 25 LINK SG CYS A 97 S2 BME A 600 1555 1555 2.04 SITE 1 AC1 6 LYS A 124 THR A 142 ASN A 144 ARG A 145 SITE 2 AC1 6 HOH A 624 HOH A 646 SITE 1 AC2 5 ILE A 3 ASN A 68 ALA A 93 CYS A 97 SITE 2 AC2 5 ILE A 100 CRYST1 61.039 61.039 97.092 90.00 90.00 120.00 P 32 2 1 6 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 0.016383 0.009459 0.000000 0.00000 SCALE2 0.000000 0.018917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010300 0.00000