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- PDB-7peg: Structure of the sporulation/germination protein YhcN from Bacill... -

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Basic information

Entry
Database: PDB / ID: 7peg
TitleStructure of the sporulation/germination protein YhcN from Bacillus subtilis
ComponentsProbable spore germination lipoprotein YhcN
KeywordsUNKNOWN FUNCTION / Sporulation / germination / Ring-Building Motif / RBM / secretion systems / YhcN / SpoIIIAG / SpoIIQ / SpoIIIAH / Bacillus subtilis
Function / homologySporulation lipoprotein YhcN/YlaJ / Sporulation lipoprotein YhcN/YlaJ-like / Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ) / sporulation resulting in formation of a cellular spore / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / Probable spore germination lipoprotein YhcN
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.77 Å
AuthorsLiu, B. / Chan, H. / Bauda, E. / Contreras-Martel, C. / Bellard, L. / Villard, A.M. / Mas, C. / Neumann, E. / Fenel, D. / Favier, A. ...Liu, B. / Chan, H. / Bauda, E. / Contreras-Martel, C. / Bellard, L. / Villard, A.M. / Mas, C. / Neumann, E. / Fenel, D. / Favier, A. / Serrano, M. / Henriques, A.O.H. / Rodrigues, C.D.A. / Morlot, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Structural insights into ring-building motif domains involved in bacterial sporulation.
Authors: Liu, B. / Chan, H. / Bauda, E. / Contreras-Martel, C. / Bellard, L. / Villard, A.M. / Mas, C. / Neumann, E. / Fenel, D. / Favier, A. / Serrano, M. / Henriques, A.O. / Rodrigues, C.D.A. / Morlot, C.
History
DepositionAug 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable spore germination lipoprotein YhcN
B: Probable spore germination lipoprotein YhcN


Theoretical massNumber of molelcules
Total (without water)37,4552
Polymers37,4552
Non-polymers00
Water2,270126
1
A: Probable spore germination lipoprotein YhcN


Theoretical massNumber of molelcules
Total (without water)18,7271
Polymers18,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable spore germination lipoprotein YhcN


Theoretical massNumber of molelcules
Total (without water)18,7271
Polymers18,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.480, 52.280, 134.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A81 - 186
2010B81 - 186

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Components

#1: Protein Probable spore germination lipoprotein YhcN


Mass: 18727.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yhcN, BSU09150 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P54598
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.5 Å3/Da / Density % sol: 17.02 %
Description: Needle-shaped crystals, dimensions of about 20 x 20 x 100 micrometers
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 20% (w/v) PEG 8,000 / PH range: 7.3-7.7

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.77→41.27 Å / Num. obs: 22053 / % possible obs: 98.3 % / Redundancy: 4.63 % / Biso Wilson estimate: 35.01 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.074 / Χ2: 0.97 / Net I/σ(I): 13.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.77-1.874.760.5572.7533020.8470.62698.4
1.87-24.720.285.4633660.9480.31698.9
2-2.164.730.1479.1931090.980.16698.6
2.16-2.374.580.09513.3429350.9890.10899
2.37-2.654.170.07515.7525230.990.08695
2.65-3.054.660.06420.0222610.9940.07298.1
3.05-3.734.810.05623.7220140.9940.06399.8
3.73-5.264.680.05124.8616160.9950.05799.6
5.26-41.274.290.05223.799270.9890.0697

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.77→41.27 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.724 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 1095 5 %RANDOM
Rwork0.2051 ---
obs0.2066 20958 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.2 Å2 / Biso mean: 41.573 Å2 / Biso min: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å2-0 Å2
2--0.16 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 1.77→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 0 126 1798
Biso mean---46.18 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171623
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.6432293
X-RAY DIFFRACTIONr_angle_other_deg1.2851.5953770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.40993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5415308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.098159
X-RAY DIFFRACTIONr_chiral_restr0.060.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021917
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
Refine LS restraints NCS

Ens-ID: 1 / Number: 3042 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 87 -
Rwork0.381 1522 -
all-1609 -
obs--98.83 %

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