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- PDB-6tad: Bd0314 DslA E143Q mutant -

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Basic information

Entry
Database: PDB / ID: 6tad
TitleBd0314 DslA E143Q mutant
ComponentsSLT domain-containing protein
KeywordsHYDROLASE / lysozyme peptidoglycan
Function / homologyTransglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Transglycosylase SLT domain-containing protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.822 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 / Category: citation / citation_author
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
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)27,8961
Polymers27,8961
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.111, 62.126, 80.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 HD100 (bacteria)
Gene: Bd0314 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MQY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.21 %
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: 1.77 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.82→62.15 Å / Num. obs: 19553 / % possible obs: 87.4 % / Redundancy: 49.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.022 / Rrim(I) all: 0.164 / Net I/σ(I): 20.1 / Num. measured all: 968126 / Scaling rejects: 1496
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.878.60.63828783330.7220.2270.6822.721.1
8.15-62.1552.80.118162753080.9950.0160.11930.299.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.822→49.28 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2101 1000 5.14 %
Rwork0.1721 --
obs0.174 19468 87.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.9 Å2 / Biso mean: 22.7483 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 1.822→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 270 1712
Biso mean---34.84 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061492
X-RAY DIFFRACTIONf_angle_d0.7892020
X-RAY DIFFRACTIONf_chiral_restr0.052212
X-RAY DIFFRACTIONf_plane_restr0.005256
X-RAY DIFFRACTIONf_dihedral_angle_d11.116888
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.822-1.9180.3372480.25499033
1.918-2.03820.26421200.2099229978
2.0382-2.19560.22541590.1806295098
2.1956-2.41650.22831830.17252976100
2.4165-2.76620.21161830.18232980100
2.7662-3.4850.191560.16883065100
3.485-49.280.19251510.15653208100

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