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- PDB-3hmb: Mutant endolysin from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3hmb
TitleMutant endolysin from Bacillus subtilis
ComponentsN-acetylmuramoyl-L-alanine amidase xlyA
KeywordsHYDROLASE / endolysin / amidase / Cell wall biogenesis/degradation / Competence / Secreted / Sporulation
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
: / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Lysin motif / LysM domain superfamily ...: / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase XlyA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.5Jul 29, 2015Group: Structure summary
Revision 1.6Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase xlyA
B: N-acetylmuramoyl-L-alanine amidase xlyA
C: N-acetylmuramoyl-L-alanine amidase xlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8636
Polymers51,6673
Non-polymers1963
Water2,684149
1
A: N-acetylmuramoyl-L-alanine amidase xlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2882
Polymers17,2221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-acetylmuramoyl-L-alanine amidase xlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2882
Polymers17,2221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: N-acetylmuramoyl-L-alanine amidase xlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2882
Polymers17,2221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.670, 152.760, 188.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase xlyA / Cell wall hydrolase / Autolysin


Mass: 17222.312 Da / Num. of mol.: 3 / Mutation: D7K, T22K, L24K, T63K, T145K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xlyA, BSU12810 / Production host: Escherichia coli (E. coli)
References: UniProt: P39800, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 4.37 Å3/Da / Density % sol: 71.88 %

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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 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 25390 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3HMA

3hma
PDB Unreleased entry


Resolution: 2.7→40 Å / Isotropic thermal model: isotropic
RfactorNum. reflection% reflection
Rfree0.2491 2511 -
Rwork0.2128 --
all-25418 -
obs-25389 99.9 %
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 3 149 3747

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