HEADER HYDROLASE (O-GLYCOSYL) 15-MAR-95 1GBS TITLE CRYSTAL STRUCTURE OF BLACK SWAN GOOSE-TYPE LYSOZYME AT 1.8 ANGSTROMS TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUSTRALIAN BLACK SWAN EGG WHITE LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYGNUS ATRATUS; SOURCE 3 ORGANISM_COMMON: BLACK SWAN; SOURCE 4 ORGANISM_TAXID: 8868 KEYWDS HYDROLASE (O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR Z.RAO,K.MACHIN,N.ISAACS REVDAT 4 20-NOV-24 1GBS 1 REMARK REVDAT 3 05-JUN-24 1GBS 1 REMARK REVDAT 2 24-FEB-09 1GBS 1 VERSN REVDAT 1 10-JUL-95 1GBS 0 JRNL AUTH Z.RAO,R.ESNOUF,N.ISAACS,D.STUART JRNL TITL A STRATEGY FOR RAPID AND EFFECTIVE REFINEMENT APPLIED TO JRNL TITL 2 BLACK SWAN LYSOZYME. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 51 331 1995 JRNL REFN ISSN 0907-4449 JRNL PMID 15299299 JRNL DOI 10.1107/S0907444994009893 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.RAO,R.ESNOUF,N.ISAACS,D.STUART REMARK 1 TITL A STRATEGY FOR RAPID AND EFFECTIVE REFINEMENT APPLIED TO REMARK 1 TITL 2 BLACK SWAN LYSOZYME REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 51 331 1995 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.RAO REMARK 1 TITL STRUCTURE DETERMINATION AND REFINEMENT OF THE GOOSE-TYPE REMARK 1 TITL 2 LYSOZYME FROM THE BLACK SWAN REMARK 1 REF THESIS, UNIVERSITY OF 1989 REMARK 1 REF 2 MELBOURNE REMARK 1 REFN ISSN 1043-1802 REMARK 1 REFERENCE 3 REMARK 1 AUTH N.ISAACS,K.MACHIN,M.MASAKUNO REMARK 1 TITL STRUCTURE OF A G-TYPE GOOSE_TYPE LYSOZYME AT 2.5 ANGSTROMS REMARK 1 TITL 2 RESOLUTION REMARK 1 REF AUST.J.BIOL.SCI. V. 38 13 1985 REMARK 1 REFN ISSN 0004-9417 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 19189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1434 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GBS 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_1000173507. 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 : 19189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 45.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.70000 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: 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 -165.34 -126.70 REMARK 500 ASP A 168 16.84 -150.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GBS A 1 185 UNP P00717 LYG_CYGAT 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 PRO ALA SER LYS THR ILE ALA GLU SEQRES 4 A 185 ARG ASP LEU LYS 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 THR ASP PHE ILE LYS ARG 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 FORMUL 2 HOH *152(H2 O) HELIX 1 1 VAL A 8 ARG A 10 5 3 HELIX 2 2 CYS A 18 GLU A 24 1 7 HELIX 3 3 GLY A 30 ARG A 47 1 18 HELIX 4 4 LYS A 49 LEU A 59 1 11 HELIX 5 5 PRO A 63 SER A 74 1 12 HELIX 6 6 GLU A 110 LYS A 130 1 21 HELIX 7 7 LYS A 136 ALA A 149 1 14 HELIX 8 8 ALA A 151 ASN A 153 5 3 HELIX 9 9 THR A 165 ASP A 167 5 3 HELIX 10 10 TYR A 169 GLN A 182 1 14 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 2.04 SSBOND 2 CYS A 18 CYS A 29 1555 1555 2.04 CRYST1 91.800 65.400 38.800 90.00 90.00 90.00 P 21 21 2 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 0.010893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025773 0.00000