HEADER HYDROLASE 19-SEP-00 1GD6 TITLE STRUCTURE OF THE BOMBYX MORI LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS LYSOZYME, 1, 4-BETA-N-ACETYLMURAMIDASE, BMLZ, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MATSUURA,T.AIZAWA,M.YAO,K.KAWANO,I.TANAKA,K.NITTA REVDAT 4 27-DEC-23 1GD6 1 REMARK REVDAT 3 24-FEB-09 1GD6 1 VERSN REVDAT 2 28-JAN-03 1GD6 1 JRNL KEYWDS REVDAT 1 21-MAR-01 1GD6 0 JRNL AUTH A.MATSUURA,M.YAO,T.AIZAWA,N.KOGANESAWA,K.MASAKI,M.MIYAZAWA, JRNL AUTH 2 M.DEMURA,I.TANAKA,K.KAWANO,K.NITTA JRNL TITL STRUCTURAL ANALYSIS OF AN INSECT LYSOZYME EXHIBITING JRNL TITL 2 CATALYTIC EFFICIENCY AT LOW TEMPERATURES. JRNL REF BIOCHEMISTRY V. 41 12086 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12356308 JRNL DOI 10.1021/BI016099J REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 7685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RAMDOM REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 550 REMARK 3 BIN R VALUE (WORKING SET) : 0.3019 REMARK 3 BIN FREE R VALUE : 0.3059 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 : 963 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.06800 REMARK 3 B22 (A**2) : 5.06800 REMARK 3 B33 (A**2) : -10.13600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.41 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.553 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.47 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINTS REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 30.26 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000005048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 283.0 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.120 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.839 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, SODIUM REMARK 280 CACODYLATE, PH 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 36.46250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.63400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.63400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.23125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.63400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.63400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.69375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.63400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.63400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.23125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.63400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.63400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.69375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 36.46250 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 ASN A 45 1.19 -63.73 REMARK 500 LYS A 69 177.35 65.12 REMARK 500 ARG A 98 -149.06 64.19 REMARK 500 HIS A 108 -20.63 -159.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GD6 A 1 119 UNP P48816 LYS_BOMMO 19 137 SEQRES 1 A 119 LYS THR PHE THR ARG CYS GLY LEU VAL HIS GLU LEU ARG SEQRES 2 A 119 LYS HIS GLY PHE GLU GLU ASN LEU MET ARG ASN TRP VAL SEQRES 3 A 119 CYS LEU VAL GLU HIS GLU SER SER ARG ASP THR SER LYS SEQRES 4 A 119 THR ASN THR ASN ARG ASN GLY SER LYS ASP TYR GLY LEU SEQRES 5 A 119 PHE GLN ILE ASN ASP ARG TYR TRP CYS SER LYS GLY ALA SEQRES 6 A 119 SER PRO GLY LYS ASP CYS ASN VAL LYS CYS SER ASP LEU SEQRES 7 A 119 LEU THR ASP ASP ILE THR LYS ALA ALA LYS CYS ALA LYS SEQRES 8 A 119 LYS ILE TYR LYS ARG HIS ARG PHE ASP ALA TRP TYR GLY SEQRES 9 A 119 TRP LYS ASN HIS CYS GLN GLY SER LEU PRO ASP ILE SER SEQRES 10 A 119 SER CYS FORMUL 2 HOH *64(H2 O) HELIX 1 1 THR A 4 HIS A 15 1 12 HELIX 2 2 GLU A 18 ASN A 20 5 3 HELIX 3 3 LEU A 21 SER A 33 1 13 HELIX 4 4 CYS A 75 LEU A 79 5 5 HELIX 5 5 ILE A 83 ARG A 98 1 16 HELIX 6 6 PHE A 99 ALA A 101 5 3 HELIX 7 7 TRP A 102 ASN A 107 1 6 SHEET 1 A 3 THR A 40 THR A 42 0 SHEET 2 A 3 LYS A 48 TYR A 50 -1 N ASP A 49 O ASN A 41 SHEET 3 A 3 ILE A 55 ASN A 56 -1 O ILE A 55 N TYR A 50 SSBOND 1 CYS A 6 CYS A 119 1555 1555 2.05 SSBOND 2 CYS A 27 CYS A 109 1555 1555 2.02 SSBOND 3 CYS A 61 CYS A 75 1555 1555 2.03 SSBOND 4 CYS A 71 CYS A 89 1555 1555 2.03 CRYST1 77.268 77.268 72.925 90.00 90.00 90.00 P 41 21 2 8 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 0.012942 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013713 0.00000