HEADER HYDROLASE 05-MAY-03 1P7S TITLE T4 LYSOZYME CORE REPACKING MUTANT V103I/TA 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: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: RR1; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHS1403 KEYWDS HYDROLASE (O-GLYCOSYL), T4 LYSOZYME, DESIGNED CORE MUTANT, AUTOMATED KEYWDS 2 PROTEIN DESIGN, PROTEIN ENGINEERING, PROTEIN FOLDING, PROTEIN KEYWDS 3 STABILITY, CORE REPACKING, BACK REVERTANT, DEAD-END ELIMINATION KEYWDS 4 THEOREM, SIDE-CHAIN PACKING, OPTIMIZED ROTAMER COMBINATIONS, ORBIT, KEYWDS 5 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.H.MOOERS,D.DATTA,W.A.BAASE,E.S.ZOLLARS,S.L.MAYO,B.W.MATTHEWS REVDAT 4 16-AUG-23 1P7S 1 REMARK REVDAT 3 27-OCT-21 1P7S 1 SEQADV REVDAT 2 24-FEB-09 1P7S 1 VERSN REVDAT 1 07-OCT-03 1P7S 0 JRNL AUTH B.H.MOOERS,D.DATTA,W.A.BAASE,E.S.ZOLLARS,S.L.MAYO, JRNL AUTH 2 B.W.MATTHEWS JRNL TITL REPACKING THE CORE OF T4 LYSOZYME BY AUTOMATED DESIGN JRNL REF J.MOL.BIOL. V. 332 741 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12963380 JRNL DOI 10.1016/S0022-2836(03)00856-8 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 23532 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. 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) : 0.192 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 625 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL 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) : 23532 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1310 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 17.163 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.143 ; 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 : TNT REMARK 3 KSOL : 0.85 REMARK 3 BSOL : 248.4 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE WORKING SET AND TEST SET WERE NOT REMARK 3 COMBINED DURING THE LAST STAGE OF REFINEMENT. REMARK 3 REMARK 3 THE OVERALL ANISOTROPIC B-VALUES ARE REMARK 3 B11=0.34, B22=-0.02, B12=B13=B23=0.0, B33=-1.32 REMARK 4 REMARK 4 1P7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019114. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.23979 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 22.086 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35100 REMARK 200 R SYM FOR SHELL (I) : 0.35100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: PDB ENTRY 1L63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M K/NA PHOSPHATE, NACL, BME, PH 6.7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.39350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.18150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.43100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.18150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.39350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.43100 REMARK 290 SMTRY3 4 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 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 5 CD GLU A 5 OE2 0.068 REMARK 500 GLU A 11 CD GLU A 11 OE2 0.066 REMARK 500 GLU A 22 CD GLU A 22 OE2 0.080 REMARK 500 REMARK 500 REMARK: NULL 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 14 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 159 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 159 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P2L RELATED DB: PDB REMARK 900 T4 LYSOZYME CORE REPACKING MUTANT V87I/TA REMARK 900 RELATED ID: 1P2R RELATED DB: PDB REMARK 900 REPACKING OF THE CORE OF T4 LYSOZYME BY AUTOMATED DESIGN REMARK 900 RELATED ID: 1P36 RELATED DB: PDB REMARK 900 REPACKING OF THE CORE OF T4 LYSOZYME BY AUTOMATED DESIGN REMARK 900 RELATED ID: 1P37 RELATED DB: PDB REMARK 900 T4 LYSOZYME CORE REPACKING BACK-REVERTANT L102M/CORE10 REMARK 900 RELATED ID: 1P3N RELATED DB: PDB REMARK 900 CORE REDESIGN BACK-REVERTANT I103V/CORE10 REMARK 900 RELATED ID: 1P64 RELATED DB: PDB REMARK 900 T4 LYSOZYME CORE REPACKING MUTANT L133F/TA REMARK 900 RELATED ID: 1P6Y RELATED DB: PDB REMARK 900 T4 LYSOZYME CORE REPACKING MUTANT M120Y/TA DBREF 1P7S A 1 164 UNP P00720 LYS_BPT4 1 164 SEQADV 1P7S THR A 54 UNP P00720 CYS 54 ENGINEERED MUTATION SEQADV 1P7S ALA A 97 UNP P00720 CYS 97 ENGINEERED MUTATION SEQADV 1P7S ILE A 103 UNP P00720 VAL 103 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 THR 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 ARG ALA ALA LEU ILE ASN MET ILE 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 FORMUL 2 HOH *177(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 ARG A 76 1 18 HELIX 4 4 ILE A 78 ASN A 81 5 4 HELIX 5 5 LEU A 84 LEU A 91 1 8 HELIX 6 6 ASP A 92 GLY A 107 1 16 HELIX 7 7 GLY A 107 GLY A 113 1 7 HELIX 8 8 PHE A 114 GLN A 123 1 10 HELIX 9 9 ARG A 125 ALA A 134 1 10 HELIX 10 10 SER A 136 THR A 142 1 7 HELIX 11 11 THR A 142 GLY A 156 1 15 HELIX 12 12 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 LEU A 32 -1 O HIS A 31 N ILE A 27 CRYST1 30.787 54.862 88.363 90.00 90.00 90.00 P 21 21 21 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 0.032481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011317 0.00000