HEADER HYDROLASE(O-GLYCOSYL) 26-JAN-94 152L TITLE CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 TITLE 2 LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: T4 LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: M13 KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR M.MATSUMURA,L.H.WEAVER,B.W.MATTHEWS REVDAT 5 06-NOV-24 152L 1 REMARK REVDAT 4 22-JUL-20 152L 1 REMARK SEQADV REVDAT 3 29-NOV-17 152L 1 HELIX REVDAT 2 24-FEB-09 152L 1 VERSN REVDAT 1 31-MAY-94 152L 0 JRNL AUTH X.J.ZHANG,B.W.MATTHEWS JRNL TITL CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF JRNL TITL 2 T4 LYSOZYME. JRNL REF PROTEIN SCI. V. 3 1031 1994 JRNL REFN ISSN 0961-8368 JRNL PMID 7920248 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.KUROKI,L.H.WEAVER,B.W.MATTHEWS REMARK 1 TITL A COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE REMARK 1 TITL 2 DISTORSION IN A MUTANT T4 LYSOZYME REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH R.H.JACOBSON,M.MATSUMURA,H.R.FABER,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF A STABILIZING DISULFIDE BRIDGE MUTANT THAT REMARK 1 TITL 2 CLOSES THE ACTIVE-SITE CLEFT OF T4 LYSOZYME REMARK 1 REF PROTEIN SCI. V. 1 46 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.E.PJURA,M.MATSUMURA,J.A.WOZNIAK,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF A THERMOSTABLE DISULFIDE-BRIDGE MUTANT OF PHAGE REMARK 1 TITL 2 T4 LYSOZYME SHOWS THAT AN ENGINEERED CROSS-LINK IN A REMARK 1 TITL 3 FLEXIBLE REGION DOES NOT INCREASE THE RIGIDITY OF THE FOLDED REMARK 1 TITL 4 PROTEIN REMARK 1 REF BIOCHEMISTRY V. 29 2592 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.MATSUMURA,G.SIGNOR,B.W.MATTHEWS REMARK 1 TITL SUBSTANTIAL INCREASE OF PROTEIN STABILITY BY MULTIPLE REMARK 1 TITL 2 DISULPHIDE BONDS REMARK 1 REF NATURE V. 342 291 1989 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 5 REMARK 1 AUTH L.H.WEAVER,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF BACTERIOPHAGE T4 LYSOZYME REFINED AT 1.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 193 189 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 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) : 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1302 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 52 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) : 0.014 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.400 ; 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 152L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING-ANODE X-RAY TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : XUONG-HAMLIN REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : AREA DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XENGEN (HOWARD, NIELSEN, XUONG) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 31.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.50000 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 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 ASP A 47 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 61 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 GLU A 108 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ASP A 20 -174.60 -66.39 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 SO4 A 200 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE ADVISORY NOTICE REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: LYCV_BPT4 REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 REMARK 999 NAME NUMBER NAME CHAIN SEQ REMARK 999 ILE 3 CYS 3 REMARK 999 ILE 9 CYS 9 REMARK 999 THR 21 CYS 21 REMARK 999 CYS 54 THR 54 REMARK 999 THR 142 CYS 142 REMARK 999 LEU 164 CYS 164 DBREF 152L A 1 163 UNP P00720 LYS_BPT4 1 163 SEQADV 152L CYS A 3 UNP P00720 ILE 3 CONFLICT SEQADV 152L CYS A 9 UNP P00720 ILE 9 CONFLICT SEQADV 152L CYS A 21 UNP P00720 THR 21 CONFLICT SEQADV 152L THR A 54 UNP P00720 CYS 54 CONFLICT SEQADV 152L CYS A 142 UNP P00720 THR 142 CONFLICT SEQRES 1 A 164 MET ASN CYS PHE GLU MET LEU ARG CYS ASP GLU GLY LEU SEQRES 2 A 164 ARG LEU LYS ILE TYR LYS ASP CYS 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 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 CYS 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 CYS HET SO4 A 200 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *52(H2 O) HELIX 1 H1 CYS A 3 GLU A 11 1 9 HELIX 2 H2 LEU A 39 ILE A 50 1 12 HELIX 3 H3 LYS A 60 ARG A 80 1 21 HELIX 4 H4 ALA A 82 SER A 90 1 9 HELIX 5 H5 ALA A 93 MET A 106 1 14 HELIX 6 H6 GLU A 108 GLY A 113 1 6 HELIX 7 H7 THR A 115 GLN A 123 1 9 HELIX 8 H8 TRP A 126 ALA A 134 1 9 HELIX 9 H9 ARG A 137 GLN A 141 1 5 HELIX 10 H10 PRO A 143 THR A 155 1 13 SHEET 1 A 3 ARG A 14 LYS A 19 0 SHEET 2 A 3 TYR A 25 GLY A 28 -1 N THR A 26 O TYR A 18 SHEET 3 A 3 HIS A 31 THR A 34 -1 N HIS A 31 O ILE A 27 SSBOND 1 CYS A 3 CYS A 97 1555 1555 1.95 SSBOND 2 CYS A 9 CYS A 164 1555 1555 2.02 SSBOND 3 CYS A 21 CYS A 142 1555 1555 1.99 SITE 1 AC1 9 CYS A 21 LYS A 83 CYS A 142 PRO A 143 SITE 2 AC1 9 ASN A 144 ARG A 145 HOH A 220 HOH A 250 SITE 3 AC1 9 HOH A 251 CRYST1 63.200 51.000 48.200 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 0.015823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020747 0.00000