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- PDB-6tab: Bd0314 DslA wild-type form 2 -

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Basic information

Entry
Database: PDB / ID: 6tab
TitleBd0314 DslA wild-type form 2
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 / Transglycosylase SLT domain-containing protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 1.2May 1, 2024Group: 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
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)28,0903
Polymers27,8971
Non-polymers1922
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-9 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.858, 64.670, 82.692
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: 27897.418 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Lithium Sulphate 0.1M Acetate pH 4.5 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.26→64.65 Å / Num. obs: 71428 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 16.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 13.2 / Num. measured all: 812815 / Scaling rejects: 707
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.26-1.297.61.852140.5090.696199.7
5.63-1011.50.0389340.9990.0110.039100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIX1refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EtoQ_mutant

Resolution: 1.26→50.94 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.501 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 3541 5 %RANDOM
Rwork0.1505 ---
obs0.1518 67048 98.64 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 66.32 Å2 / Biso mean: 19.704 Å2 / Biso min: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.26→50.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 10 246 1699
Biso mean--33.61 36.43 -
Num. residues----182
LS refinement shellResolution: 1.26→1.292 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.394 237 -
Rwork0.372 4797 -
obs--96.46 %

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