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- PDB-6taf: Bd0314 DslA E154Q mutant -

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Basic information

Entry
Database: PDB / ID: 6taf
TitleBd0314 DslA E154Q mutant
ComponentsSLT domain-containing protein
KeywordsHYDROLASE / lysozyme peptidoglycan
Function / homologyTransglycosylase SLT domain 1 / Transglycosylase SLT domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily / ACETATE ION / Transglycosylase SLT domain-containing protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.336 Å
AuthorsLovering, A.L. / Harding, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Councilstudentship United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: A lysozyme with altered substrate specificity facilitates prey cell exit by the periplasmic predator Bdellovibrio bacteriovorus.
Authors: Harding, C.J. / Huwiler, S.G. / Somers, H. / Lambert, C. / Ray, L.J. / Till, R. / Taylor, G. / Moynihan, P.J. / Sockett, R.E. / Lovering, A.L.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
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 / _software.name
Revision 1.2May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: SLT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3406
Polymers27,8961
Non-polymers4435
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-35 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.729, 47.854, 49.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SLT domain-containing protein


Mass: 27896.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd0314 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MQY8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.79 Å3/Da / Density % sol: 31.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M lithium sulphate 0.1M sodium citrate pH 5.5 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.336→100 Å / Num. obs: 45432 / % possible obs: 98.4 % / Redundancy: 12.5 % / CC1/2: 0.994 / Net I/σ(I): 12.2
Reflection shellResolution: 1.37→1.38 Å / Num. unique obs: 2267 / CC1/2: 0.617

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mutant protein

Resolution: 1.336→34.308 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.1951 2260 4.98 %
Rwork0.1771 --
obs0.178 45425 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.89 Å2 / Biso mean: 17.8606 Å2 / Biso min: 5.4 Å2
Refinement stepCycle: final / Resolution: 1.336→34.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 15 219 1677
Biso mean--49.55 30.34 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051546
X-RAY DIFFRACTIONf_angle_d1.0442095
X-RAY DIFFRACTIONf_chiral_restr0.073218
X-RAY DIFFRACTIONf_plane_restr0.005264
X-RAY DIFFRACTIONf_dihedral_angle_d11.583558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.336-1.36450.22841300.22992731100
1.3645-1.39630.21671700.21932663100
1.3963-1.43120.24271490.21042680100
1.4312-1.46990.21631470.20092681100
1.4699-1.51320.20061220.18572745100
1.5132-1.5620.21371160.18272756100
1.562-1.61780.1791080.16412726100
1.6178-1.68260.2021620.16392707100
1.6826-1.75920.20641530.16992735100
1.7592-1.85190.18861230.17122740100
1.8519-1.96790.19131320.1686223983
1.9679-2.11990.17471450.1622258095
2.1199-2.33310.17641620.1633264997
2.3331-2.67060.20721470.1732776100
2.6706-3.36430.19861460.18262805100
3.3643-34.3080.18841480.1782952100

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