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- PDB-3hmc: Endolysin from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3hmc
TitleEndolysin from Bacillus anthracis
ComponentsPutative prophage LambdaBa04, glycosyl hydrolase, family 25
KeywordsHYDROLASE / endolysin / glycosyl hydrolase
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity
Similarity search - Function
N-acetylmuramoyl-l-alanine amidase, C-terminal domain / PlyG Cell wall binding domain / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endolysin / Putative prophage LambdaBa04, glycosyl hydrolase, family 25
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.44 Å
AuthorsLow, L.Y. / Liddington, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins.
Authors: Low, L.Y. / Yang, C. / Perego, M. / Osterman, A. / Liddington, R.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Aug 17, 2011Group: Database references
Revision 1.4Dec 21, 2011Group: Database references
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative prophage LambdaBa04, glycosyl hydrolase, family 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8332
Polymers21,6381
Non-polymers1951
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.682, 56.454, 67.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative prophage LambdaBa04, glycosyl hydrolase, family 25 / Prophage LambdaBa04 / glycosyl hydrolase / family 25 / putative


Mass: 21637.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS0460, BA_0485, GBAA0485, GBAA_0485 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81YZ2, UniProt: A0A6L7HQ02*PLUS
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.14 Å3/Da / Density % sol: 42.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 35073 / % possible obs: 95.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 31.4
Reflection shellResolution: 1.44→1.46 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.44→30 Å / Isotropic thermal model: anisotropic
RfactorNum. reflection% reflection
Rfree0.2279 1732 -
Rwork0.2071 --
all-37265 -
obs-32736 94.1 %
Refinement stepCycle: LAST / Resolution: 1.44→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 12 231 1753

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