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- PDB-6v4v: The crystal structure of BonA from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6v4v
TitleThe crystal structure of BonA from Acinetobacter baumannii
ComponentsBON domain protein
KeywordsLIPID BINDING PROTEIN / Periplasmic / Lipoprotein / Divisome Protein / Cell Motility / Outer-membrane stability
Function / homologyBON domain profile. / BON domain / BON domain / BON domain protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsGrinter, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z Australia
CitationJournal: Mbio / Year: 2021
Title: BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function.
Authors: Grinter, R. / Morris, F.C. / Dunstan, R.A. / Leung, P.M. / Kropp, A. / Belousoff, M. / Gunasinghe, S.D. / Scott, N.E. / Beckham, S. / Peleg, A.Y. / Greening, C. / Li, J. / Heinz, E. / Lithgow, T.
History
DepositionDec 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: BON domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9085
Polymers20,6471
Non-polymers2624
Water2,756153
1
A: BON domain protein
hetero molecules

A: BON domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,81710
Polymers41,2932
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area3990 Å2
ΔGint-253 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.052, 60.052, 99.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-395-

HOH

31A-408-

HOH

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Components

#1: Protein BON domain protein / BON domain-containing protein / Outer membrane lipoprotein / Periplasmic or secreted lipoprotein


Mass: 20646.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M79_12275 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: V5VFJ0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.2 M Zn Acetate, 0.1 M Na Acetate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 17, 2016 / Details: Yes
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.65→46.07 Å / Num. obs: 25589 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Net I/σ(I): 24.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.675 / Num. unique obs: 1254 / CC1/2: 0.693 / Rpim(I) all: 0.777 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→35.904 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2124 1294 5.07 %
Rwork0.1883 --
obs0.1895 25542 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.69 Å2 / Biso mean: 38.1331 Å2 / Biso min: 18.6 Å2
Refinement stepCycle: final / Resolution: 1.65→35.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 4 153 1260
Biso mean--45.77 48.46 -
Num. residues----143
Refinement TLS params.Method: refined / Origin x: 9.2099 Å / Origin y: 47.0654 Å / Origin z: 39.8639 Å
111213212223313233
T0.183 Å2-0.0046 Å20.0271 Å2-0.2468 Å2-0.0014 Å2--0.1946 Å2
L2.5571 °20.416 °2-0.61 °2-0.9759 °2-0.106 °2--1.8783 °2
S-0.1874 Å °0.07 Å °-0.0341 Å °0.0528 Å °0.039 Å °0.1763 Å °0.1522 Å °-0.4291 Å °0.1274 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 151
2X-RAY DIFFRACTION1allS3 - 162
3X-RAY DIFFRACTION1allB1 - 3
4X-RAY DIFFRACTION1allB4

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