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- PDB-6o59: Crystal structure of the N-terminal domain of the A subunit of th... -

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Basic information

Entry
Database: PDB / ID: 6o59
TitleCrystal structure of the N-terminal domain of the A subunit of the Bacillus megaterium spore germinant receptor GerK3
ComponentsGermination protein
KeywordsTRANSPORT PROTEIN / Bacillus / spores / spore germination / spore germinant recepter
Function / homologyBacillus/Clostridium Ger spore germination protein / Bacillus/Clostridium GerA spore germination protein / spore germination / membrane => GO:0016020 / plasma membrane / Germination protein
Function and homology information
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsLi, Y. / Hao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)W911NF-09-1-0286 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural and functional analyses of the N-terminal domain of the A subunit of aBacillus megateriumspore germinant receptor.
Authors: Li, Y. / Jin, K. / Perez-Valdespino, A. / Federkiewicz, K. / Davis, A. / Maciejewski, M.W. / Setlow, P. / Hao, B.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Germination protein
B: Germination protein


Theoretical massNumber of molelcules
Total (without water)60,1072
Polymers60,1072
Non-polymers00
Water2,090116
1
A: Germination protein


Theoretical massNumber of molelcules
Total (without water)30,0531
Polymers30,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Germination protein


Theoretical massNumber of molelcules
Total (without water)30,0531
Polymers30,0531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-20 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.245, 106.245, 140.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Germination protein / GerK3A


Mass: 30053.373 Da / Num. of mol.: 2 / Mutation: N-terminal domain (residues 26-296)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: gerAA / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O07504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.15 M lithium sulfate, 10-15% PEG6000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.075
SYNCHROTRONNSLS-II 17-ID-120.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 10, 2015
DECTRIS EIGER X 9M2PIXELMar 28, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.97921
ReflectionResolution: 2.79→50 Å / Num. obs: 20443 / % possible obs: 99.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 92.26 Å2 / Rsym value: 0.078 / Net I/σ(I): 21
Reflection shellResolution: 2.79→2.85 Å / Rmerge(I) obs: 0.821

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.372 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1053 5.15 %RANDOM
Rwork0.205 ---
obs0.206 20443 99.4 %-
Displacement parametersBiso max: 210.54 Å2 / Biso mean: 87.32 Å2 / Biso min: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.424 Å20 Å20 Å2
2---9.424 Å20 Å2
3---18.848 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.79→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 116 3081
Biso mean---84.91 -
Num. residues----381
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1439SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3024HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion428SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3393SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3024HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4098HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion3.41
LS refinement shellResolution: 2.79→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3354 22 5.38 %
Rwork0.2627 387 -
all0.2666 409 -
obs--93.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.49570.9452-0.23524.17980.84213.0368-0.0424-0.2233-0.62120.2680.1141-0.54550.38990.6342-0.0717-0.13480.1771-0.1615-0.04-0.0244-0.0953.962455.930650.6465
23.5677-1.2404-1.1692.73361.31933.15190.1394-0.0747-0.24380.2869-0.25680.24540.4936-0.17760.1174-0.0138-0.0709-0.0014-0.0849-0.0495-0.142921.251859.772852.1732
32.2894-1.8522-2.09383.09331.18244.2169-0.01860.0554-0.1250.11240.05450.12330.261-0.2172-0.0359-0.1891-0.12160.04810.0307-0.0982-0.0998.471773.710259.5826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|25 - A|152 }A25 - 152
2X-RAY DIFFRACTION2{ A|170 - A|296 }A170 - 296
3X-RAY DIFFRACTION3{ B|171 - B|296 }B171 - 296

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