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- PDB-6fxp: Crystal structure of S. aureus glucosaminidase B -

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Basic information

Entry
Database: PDB / ID: 6fxp
TitleCrystal structure of S. aureus glucosaminidase B
ComponentsUncharacterized protein
KeywordsHYDROLASE / lysozyme-like fold / N-acetylglucosaminidase / peptidoglycan hydrolase / GH73
Function / homologyLysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / amidase activity / membrane => GO:0016020 / extracellular region / LYZ2 domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsPintar, S. / Turk, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
ARRSP1-0048 Slovenia
CitationJournal: Commun Biol / Year: 2020
Title: Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis.
Authors: Pintar, S. / Borisek, J. / Usenik, A. / Perdih, A. / Turk, D.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,64713
Polymers57,9992
Non-polymers1,64811
Water9,872548
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0298
Polymers29,0001
Non-polymers1,0307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6185
Polymers29,0001
Non-polymers6184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.77, 151.77, 122.51
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-749-

HOH

21B-846-

HOH

31B-871-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 28999.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: SAV1775 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JSV1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.75 / Details: 0.1 M Na3 citrate, 45 % PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.89429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.03→47.66 Å / Num. obs: 53891 / % possible obs: 99.8 % / Redundancy: 18.3 % / Rrim(I) all: 0.091 / Net I/σ(I): 27
Reflection shellResolution: 2.03→2.15 Å

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Processing

Software
NameClassification
MAINrefinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→19.95 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9351 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 -100 %NONE
Rwork0.212 ---
all0.212 ---
obs0.212 53814 100 %-
Solvent computationBsol: 35.11 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 132.07 Å2 / Biso mean: 41.39 Å2 / Biso min: 20.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.1 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 107 548 4701
LS refinement shellResolution: 2.03→2.07 Å /
RfactorNum. reflection
Rfree0.3159 -
Rwork0.3029 2544

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