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- PDB-1jfx: Crystal structure of the bacterial lysozyme from Streptomyces coe... -

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Basic information

Entry
Database: PDB / ID: 1jfx
TitleCrystal structure of the bacterial lysozyme from Streptomyces coelicolor at 1.65 A resolution
Components1,4-beta-N-Acetylmuramidase M1
KeywordsHYDROLASE / beta-alpha-barrel / Cellosyl / lysozyme / N-acetylmuramidase
Function / homology
Function and homology information


cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to bacterium / extracellular region
Similarity search - Function
Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.65 Å
AuthorsRau, A. / Hogg, T. / Marquardt, R. / Hilgenfeld, R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: A new lysozyme fold. Crystal structure of the muramidase from Streptomyces coelicolor at 1.65 A resolution.
Authors: Rau, A. / Hogg, T. / Marquardt, R. / Hilgenfeld, R.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999 SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS IDENTIFIED FOR 1,4-BETA-N-ACETYLMURAMIDASE M1 OF ... SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS IDENTIFIED FOR 1,4-BETA-N-ACETYLMURAMIDASE M1 OF STREPTOMYCES COELICOLOR. THE DATABASE REFERENCE LISTED IS FOR THE CORRESPONDING PROTEIN IN A CLOSELY RELATED SPECIES OF STREPTOMYCES BACTERIA, STREPTOMYCES GLOBISPORUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-beta-N-Acetylmuramidase M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9329
Polymers23,6481
Non-polymers2848
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.15, 38.22, 51.04
Angle α, β, γ (deg.)90.00, 108.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 1,4-beta-N-Acetylmuramidase M1 / BETA-1 / 4-N / 6-O-DIACETYLMURAMIDASE


Mass: 23647.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cel / Production host: Streptomyces coelicolor (bacteria) / Strain (production host): HP1 / References: UniProt: P25310, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMsodium phosphate1drop
3100 mM1dropNaCl
41.6 Mammonium sulfate1reservoir
510 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 28, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 24126 / Num. obs: 94866 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 8.5 / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 24126 / Num. measured all: 94866

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.65→35.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1164171.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1214 5 %RANDOM
Rwork0.152 ---
all-24126 --
obs-24126 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.28 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.19 Å2
2--0.7 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.65→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 8 399 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it0.871.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it2.053
X-RAY DIFFRACTIONc_scangle_it2.665
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 189 4.9 %
Rwork0.209 3682 -
obs-3682 94.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it5
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.209

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