HEADER HYDROLASE(O-GLYCOSYL) 05-MAY-94 154L TITLE THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A BOUND TITLE 2 TRISACCHARIDE SHOW THAT THE "GOOSE-TYPE LYSOZYMES LACK A CATALYTIC TITLE 3 ASPARTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOOSE LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR L.H.WEAVER,M.G.GRUETTER,B.W.MATTHEWS REVDAT 5 20-NOV-24 154L 1 HETSYN REVDAT 4 29-JUL-20 154L 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 154L 1 VERSN REVDAT 2 24-FEB-09 154L 1 VERSN REVDAT 1 26-JAN-95 154L 0 JRNL AUTH L.H.WEAVER,M.G.GRUTTER,B.W.MATTHEWS JRNL TITL THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX JRNL TITL 2 WITH A BOUND TRISACCHARIDE SHOW THAT THE "GOOSE-TYPE" JRNL TITL 3 LYSOZYMES LACK A CATALYTIC ASPARTATE RESIDUE. JRNL REF J.MOL.BIOL. V. 245 54 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7823320 JRNL DOI 10.1016/S0022-2836(95)80038-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.H.WEAVER,B.W.MATTHEWS REMARK 1 TITL THE 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 21303 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) : 0.159 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 : 1432 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 164 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) : 0.017 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.500 ; 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 154L 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_1000170125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL 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: NULL 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 (%): 49.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 32.70000 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, B 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 24 CD GLU A 24 OE2 0.071 REMARK 500 GLU A 57 CD GLU A 57 OE1 0.085 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 ASP A 3 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 3 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 41 CB - CG - OD1 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 86 CB - CG - OD1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ASP A 86 CB - CG - OD2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 97 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 97 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -3.2 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 CYS A 29 -169.17 -127.28 REMARK 500 ASP A 168 16.46 -151.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 154L A 1 185 UNP P00718 LYG_ANSAN 1 185 SEQRES 1 A 185 ARG THR ASP CYS TYR GLY ASN VAL ASN ARG ILE ASP THR SEQRES 2 A 185 THR GLY ALA SER CYS LYS THR ALA LYS PRO GLU GLY LEU SEQRES 3 A 185 SER TYR CYS GLY VAL SER ALA SER LYS LYS ILE ALA GLU SEQRES 4 A 185 ARG ASP LEU GLN ALA MET ASP ARG TYR LYS THR ILE ILE SEQRES 5 A 185 LYS LYS VAL GLY GLU LYS LEU CYS VAL GLU PRO ALA VAL SEQRES 6 A 185 ILE ALA GLY ILE ILE SER ARG GLU SER HIS ALA GLY LYS SEQRES 7 A 185 VAL LEU LYS ASN GLY TRP GLY ASP ARG GLY ASN GLY PHE SEQRES 8 A 185 GLY LEU MET GLN VAL ASP LYS ARG SER HIS LYS PRO GLN SEQRES 9 A 185 GLY THR TRP ASN GLY GLU VAL HIS ILE THR GLN GLY THR SEQRES 10 A 185 THR ILE LEU ILE ASN PHE ILE LYS THR ILE GLN LYS LYS SEQRES 11 A 185 PHE PRO SER TRP THR LYS ASP GLN GLN LEU LYS GLY GLY SEQRES 12 A 185 ILE SER ALA TYR ASN ALA GLY ALA GLY ASN VAL ARG SER SEQRES 13 A 185 TYR ALA ARG MET ASP ILE GLY THR THR HIS ASP ASP TYR SEQRES 14 A 185 ALA ASN ASP VAL VAL ALA ARG ALA GLN TYR TYR LYS GLN SEQRES 15 A 185 HIS GLY TYR HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 HOH *164(H2 O) HELIX 1 1 ASN A 7 ILE A 11 5 5 HELIX 2 2 SER A 17 LYS A 22 1 6 HELIX 3 3 GLY A 30 ASP A 41 1 12 HELIX 4 4 ASP A 41 ARG A 47 1 7 HELIX 5 5 TYR A 48 CYS A 60 1 13 HELIX 6 6 GLU A 62 HIS A 75 1 14 HELIX 7 7 ALA A 76 LYS A 78 5 3 HELIX 8 8 GLY A 109 PHE A 131 1 23 HELIX 9 9 THR A 135 GLY A 150 1 16 HELIX 10 10 ALA A 151 VAL A 154 5 4 HELIX 11 11 THR A 164 ASP A 167 5 4 HELIX 12 12 ASP A 168 HIS A 183 1 16 SHEET 1 A 2 GLY A 90 PHE A 91 0 SHEET 2 A 2 VAL A 96 ASP A 97 -1 O VAL A 96 N PHE A 91 SSBOND 1 CYS A 4 CYS A 60 1555 1555 2.06 SSBOND 2 CYS A 18 CYS A 29 1555 1555 2.06 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.41 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.40 CRYST1 38.300 65.400 44.700 90.00 117.00 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 0.026110 0.000000 0.013304 0.00000 SCALE2 0.000000 0.015291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025108 0.00000