HEADER HYDROLASE 22-JUN-01 1JFX TITLE CRYSTAL STRUCTURE OF THE BACTERIAL LYSOZYME FROM TITLE 2 STREPTOMYCES COELICOLOR AT 1.65 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1,4-BETA-N-ACETYLMURAMIDASE M1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-1,4-N,6-O-DIACETYLMURAMIDASE; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 1902; SOURCE 4 GENE: CEL; SOURCE 5 EXPRESSION_SYSTEM: STREPTOMYCES COELICOLOR; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1902; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HP1 KEYWDS BETA-ALPHA-BARREL, CELLOSYL, LYSOZYME, N-ACETYLMURAMIDASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RAU,T.HOGG,R.MARQUARDT,R.HILGENFELD REVDAT 3 24-FEB-09 1JFX 1 VERSN REVDAT 2 01-APR-03 1JFX 1 JRNL REVDAT 1 05-SEP-01 1JFX 0 JRNL AUTH A.RAU,T.HOGG,R.MARQUARDT,R.HILGENFELD JRNL TITL A NEW LYSOZYME FOLD. CRYSTAL STRUCTURE OF THE JRNL TITL 2 MURAMIDASE FROM STREPTOMYCES COELICOLOR AT 1.65 A JRNL TITL 3 RESOLUTION. JRNL REF J.BIOL.CHEM. V. 276 31994 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11427528 JRNL DOI 10.1074/JBC.M102591200 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1164171.270 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 24126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1214 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3682 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 189 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1672 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 399 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.90 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.870 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.050 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.660 ; 5.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 32.28 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 1JFX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94866 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, HEPES, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 55.57500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.57500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.11000 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 ASN A 39 19.03 -147.94 REMARK 500 ASP A 89 24.44 -151.58 REMARK 500 ASN A 90 -3.13 67.15 REMARK 500 THR A 132 -4.43 77.78 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 CL A 1001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1002 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1003 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1004 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1006 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1007 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1008 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1009 REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMARK 999 NO DATABASE REFERENCE SEQUENCE WAS IDENTIFIED FOR REMARK 999 1,4-BETA-N-ACETYLMURAMIDASE M1 OF STREPTOMYCES REMARK 999 COELICOLOR. THE DATABASE REFERENCE LISTED IS REMARK 999 FOR THE CORRESPONDING PROTEIN IN A CLOSELY RELATED REMARK 999 SPECIES OF STREPTOMYCES BACTERIA, STREPTOMYCES REMARK 999 GLOBISPORUS. DBREF 1JFX A 1 217 UNP P25310 LYSM1_STRGL 78 294 SEQRES 1 A 217 ASP THR SER GLY VAL GLN GLY ILE ASP VAL SER HIS TRP SEQRES 2 A 217 GLN GLY SER ILE ASN TRP SER SER VAL LYS SER ALA GLY SEQRES 3 A 217 MET SER PHE ALA TYR ILE LYS ALA THR GLU GLY THR ASN SEQRES 4 A 217 TYR LYS ASP ASP ARG PHE SER ALA ASN TYR THR ASN ALA SEQRES 5 A 217 TYR ASN ALA GLY ILE ILE ARG GLY ALA TYR HIS PHE ALA SEQRES 6 A 217 ARG PRO ASN ALA SER SER GLY THR ALA GLN ALA ASP TYR SEQRES 7 A 217 PHE ALA SER ASN GLY GLY GLY TRP SER ARG ASP ASN ARG SEQRES 8 A 217 THR LEU PRO GLY VAL LEU ASP ILE GLU HIS ASN PRO SER SEQRES 9 A 217 GLY ALA MET CYS TYR GLY LEU SER THR THR GLN MET ARG SEQRES 10 A 217 THR TRP ILE ASN ASP PHE HIS ALA ARG TYR LYS ALA ARG SEQRES 11 A 217 THR THR ARG ASP VAL VAL ILE TYR THR THR ALA SER TRP SEQRES 12 A 217 TRP ASN THR CYS THR GLY SER TRP ASN GLY MET ALA ALA SEQRES 13 A 217 LYS SER PRO PHE TRP VAL ALA HIS TRP GLY VAL SER ALA SEQRES 14 A 217 PRO THR VAL PRO SER GLY PHE PRO THR TRP THR PHE TRP SEQRES 15 A 217 GLN TYR SER ALA THR GLY ARG VAL GLY GLY VAL SER GLY SEQRES 16 A 217 ASP VAL ASP ARG ASN LYS PHE ASN GLY SER ALA ALA ARG SEQRES 17 A 217 LEU LEU ALA LEU ALA ASN ASN THR ALA HET CL A1001 1 HET CL A1002 1 HET CL A1003 1 HET CL A1004 1 HET CL A1006 1 HET CL A1007 1 HET CL A1008 1 HET CL A1009 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 8(CL 1-) FORMUL 10 HOH *398(H2 O) HELIX 1 1 SER A 11 GLY A 15 5 5 HELIX 2 2 ASN A 18 ALA A 25 1 8 HELIX 3 3 ARG A 44 ALA A 55 1 12 HELIX 4 4 SER A 71 ASN A 82 1 12 HELIX 5 5 SER A 112 THR A 132 1 21 HELIX 6 6 THR A 140 GLY A 149 1 10 HELIX 7 7 SER A 205 ASN A 215 1 11 SHEET 1 A10 TYR A 40 LYS A 41 0 SHEET 2 A10 PHE A 29 GLU A 36 -1 O GLU A 36 N TYR A 40 SHEET 3 A10 GLN A 6 VAL A 10 1 O GLN A 6 N PHE A 29 SHEET 4 A10 VAL A 193 PHE A 202 -1 O ASP A 198 N ASP A 9 SHEET 5 A10 PHE A 181 VAL A 190 -1 N TRP A 182 O LYS A 201 SHEET 6 A10 PHE A 160 ALA A 163 1 O PHE A 160 N PHE A 181 SHEET 7 A10 VAL A 136 THR A 139 1 O ILE A 137 N TRP A 161 SHEET 8 A10 VAL A 96 ASP A 98 1 N LEU A 97 O VAL A 136 SHEET 9 A10 ILE A 58 PHE A 64 1 O ALA A 61 N VAL A 96 SHEET 10 A10 PHE A 29 GLU A 36 1 O ALA A 30 N GLY A 60 SSBOND 1 CYS A 108 CYS A 147 1555 1555 2.03 SITE 1 AC1 3 GLY A 188 ARG A 189 ARG A 199 SITE 1 AC2 2 TRP A 179 HOH A1025 SITE 1 AC3 3 ARG A 133 ASP A 134 ASN A 215 SITE 1 AC4 5 ARG A 199 SER A 205 ALA A 207 HOH A1173 SITE 2 AC4 5 HOH A1306 SITE 1 AC5 2 ASN A 152 HOH A1140 SITE 1 AC6 3 ASN A 68 ASN A 102 HOH A1087 SITE 1 AC7 5 THR A 38 SER A 70 ALA A 74 HOH A1079 SITE 2 AC7 5 HOH A1322 SITE 1 AC8 2 HOH A1259 HOH A1390 CRYST1 111.150 38.220 51.040 90.00 108.36 90.00 C 1 2 1 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 0.008997 0.000000 0.002986 0.00000 SCALE2 0.000000 0.026165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020645 0.00000