HEADER HYDROLASE 10-DEC-06 2O7A TITLE T4 LYSOZYME C-TERMINAL FRAGMENT 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 GENE: E; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA/PLACI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET27K KEYWDS PROTEIN FOLDING, PROTEIN STABILITY, LYSOZYME, CIRCULAR PERMUTANT, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.ECHOLS,E.KWON,S.M.MARQUSEE,T.ALBER REVDAT 7 20-OCT-21 2O7A 1 REMARK SEQADV REVDAT 6 24-JUL-19 2O7A 1 REMARK LINK REVDAT 5 18-OCT-17 2O7A 1 REMARK REVDAT 4 02-AUG-17 2O7A 1 SOURCE REMARK REVDAT 3 24-FEB-09 2O7A 1 VERSN REVDAT 2 08-MAY-07 2O7A 1 JRNL REVDAT 1 10-APR-07 2O7A 0 JRNL AUTH J.CELLITTI,M.LLINAS,N.ECHOLS,E.A.SHANK,B.GILLESPIE,E.KWON, JRNL AUTH 2 S.M.CROWDER,F.W.DAHLQUIST,T.ALBER,S.MARQUSEE JRNL TITL EXPLORING SUBDOMAIN COOPERATIVITY IN T4 LYSOZYME I: JRNL TITL 2 STRUCTURAL AND ENERGETIC STUDIES OF A CIRCULAR PERMUTANT AND JRNL TITL 3 PROTEIN FRAGMENT. JRNL REF PROTEIN SCI. V. 16 842 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17400926 JRNL DOI 10.1110/PS.062628607 REMARK 2 REMARK 2 RESOLUTION. 0.84 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) : 0.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.090 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.108 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4630 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 92310 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 941 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.037 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.049 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL 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 2O7A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.82653 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92458 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 31.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22400 REMARK 200 R SYM FOR SHELL (I) : 0.22400 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1SX7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NACACODYLATE PH 5.0, 200 MM REMARK 280 NAACETATE, 26% PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 25.00850 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 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 ASN A 163 REMARK 465 LEU A 164 REMARK 465 SER A 165 REMARK 465 GLY A 166 REMARK 465 GLY A 167 REMARK 465 GLY A 168 REMARK 465 GLY A 169 REMARK 465 ALA A 170 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 76 CD - NE - CZ ANGL. DEV. = 22.4 DEGREES REMARK 500 LYS A 85 CD - CE - NZ ANGL. DEV. = 14.4 DEGREES REMARK 500 THR A 115 OG1 - CB - CG2 ANGL. DEV. = -30.5 DEGREES REMARK 500 ARG A 119 CD - NE - CZ ANGL. DEV. = 27.9 DEGREES REMARK 500 ARG A 119 NH1 - CZ - NH2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET A 171 CA - CB - CG ANGL. DEV. = -14.4 DEGREES REMARK 500 MET A 171 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 GLU A 175 OE1 - CD - OE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 178 CD - NE - CZ ANGL. DEV. = 10.6 DEGREES 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 ACT A 425 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 426 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O4W RELATED DB: PDB REMARK 900 T4 LYSOZYME CIRCULAR PERMUTANT REMARK 900 RELATED ID: 2O79 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 171-182 CORRESPOND TO RESIDUES 1-12 IN REMARK 999 THE WILD-TYPE STRUCTURE. THE INITIAL 12 RESIDUES REMARK 999 HAVE BEEN MOVED TO THE C-TERMINUS, WITH A 6-RESIDUE REMARK 999 LINKER (SGGGGA) IN BETWEEN. DBREF 2O7A A 60 164 UNP P00720 LYS_BPT4 60 164 DBREF 2O7A A 171 182 UNP P00720 LYS_BPT4 1 12 SEQADV 2O7A SME A 59 UNP P00720 CLONING ARTIFACT SEQADV 2O7A ALA A 97 UNP P00720 CYS 97 ENGINEERED MUTATION SEQADV 2O7A SER A 165 UNP P00720 LINKER SEQADV 2O7A GLY A 166 UNP P00720 LINKER SEQADV 2O7A GLY A 167 UNP P00720 LINKER SEQADV 2O7A GLY A 168 UNP P00720 LINKER SEQADV 2O7A GLY A 169 UNP P00720 LINKER SEQADV 2O7A ALA A 170 UNP P00720 LINKER SEQADV 2O7A ASP A 172 UNP P00720 ENGINEERED MUTATION SEQRES 1 A 124 SME LYS ASP GLU ALA GLU LYS LEU PHE ASN GLN ASP VAL SEQRES 2 A 124 ASP ALA ALA VAL ARG GLY ILE LEU ARG ASN ALA LYS LEU SEQRES 3 A 124 LYS PRO VAL TYR ASP SER LEU ASP ALA VAL ARG ARG ALA SEQRES 4 A 124 ALA LEU ILE ASN MET VAL PHE GLN MET GLY GLU THR GLY SEQRES 5 A 124 VAL ALA GLY PHE THR ASN SER LEU ARG MET LEU GLN GLN SEQRES 6 A 124 LYS ARG TRP ASP GLU ALA ALA VAL ASN LEU ALA LYS SER SEQRES 7 A 124 ARG TRP TYR ASN GLN THR PRO ASN ARG ALA LYS ARG VAL SEQRES 8 A 124 ILE THR THR PHE ARG THR GLY THR TRP ASP ALA TYR LYS SEQRES 9 A 124 ASN LEU SER GLY GLY GLY GLY ALA MET ASP ILE PHE GLU SEQRES 10 A 124 MET LEU ARG ILE ASP GLU GLY MODRES 2O7A SME A 59 MET METHIONINE SULFOXIDE HET SME A 59 18 HET ACT A 425 4 HET CL A 426 1 HETNAM SME METHIONINE SULFOXIDE HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 1 SME C5 H11 N O3 S FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 CL CL 1- FORMUL 4 HOH *330(H2 O) HELIX 1 1 ASP A 61 LYS A 65 5 5 HELIX 2 2 PHE A 67 ARG A 80 1 14 HELIX 3 3 LEU A 84 LEU A 91 1 8 HELIX 4 4 ASP A 92 GLY A 107 1 16 HELIX 5 5 GLY A 107 GLY A 113 1 7 HELIX 6 6 PHE A 114 GLN A 123 1 10 HELIX 7 7 ARG A 125 ALA A 134 1 10 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 ASP A 172 GLY A 182 1 11 LINK C ASME A 59 N LYS A 60 1555 1555 1.34 LINK C BSME A 59 N LYS A 60 1555 1555 1.34 SITE 1 AC1 4 ARG A 178 HOH A 572 HOH A 626 HOH A 688 SITE 1 AC2 6 THR A 142 PRO A 143 ASN A 144 ARG A 145 SITE 2 AC2 6 HOH A 475 HOH A 541 CRYST1 31.634 50.017 32.711 90.00 90.86 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 0.031612 0.000000 0.000475 0.00000 SCALE2 0.000000 0.019993 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030574 0.00000 MASTER 232 0 3 10 0 0 3 6 0 0 0 10 END