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- PDB-6nq8: Crystal structure of YetJ mutant from Bacillus Subtilis - D171E -

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Basic information

Entry
Database: PDB / ID: 6nq8
TitleCrystal structure of YetJ mutant from Bacillus Subtilis - D171E
ComponentsUncharacterized protein YetJ
KeywordsMEMBRANE PROTEIN / Ca2+ channel structure / open conformation / pH sensor
Function / homologyBax inhibitor 1-related / Inhibitor of apoptosis-promoting Bax1 / regulation of proteolysis / calcium channel activity / calcium ion transport / membrane / plasma membrane / pH-sensitive calcium channel
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGuo, G. / Chang, Y. / Liu, Q.
CitationJournal: Structure / Year: 2019
Title: Ion and pH Sensitivity of a TMBIM Ca2+Channel.
Authors: Guo, G. / Xu, M. / Chang, Y. / Luyten, T. / Seitaj, B. / Liu, W. / Zhu, P. / Bultynck, G. / Shi, L. / Quick, M. / Liu, Q.
History
DepositionJan 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YetJ
B: Uncharacterized protein YetJ
C: Uncharacterized protein YetJ
D: Uncharacterized protein YetJ


Theoretical massNumber of molelcules
Total (without water)95,4344
Polymers95,4344
Non-polymers00
Water00
1
A: Uncharacterized protein YetJ


Theoretical massNumber of molelcules
Total (without water)23,8591
Polymers23,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein YetJ


Theoretical massNumber of molelcules
Total (without water)23,8591
Polymers23,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein YetJ


Theoretical massNumber of molelcules
Total (without water)23,8591
Polymers23,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein YetJ


Theoretical massNumber of molelcules
Total (without water)23,8591
Polymers23,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.090, 117.296, 52.407
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein YetJ


Mass: 23858.578 Da / Num. of mol.: 4 / Mutation: D171E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yetJ, BSU07200
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O31539

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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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MOPS, pH 7.5, 38% PEG 400, and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→47.15 Å / Num. obs: 76248 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 5.4
Reflection shellResolution: 3.1→3.31 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PGS

4pgs


Resolution: 3.1→39.082 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.57
RfactorNum. reflection% reflection
Rfree0.2705 1219 5.16 %
Rwork0.2431 --
obs0.2446 23641 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 0 0 6422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026592
X-RAY DIFFRACTIONf_angle_d0.4548969
X-RAY DIFFRACTIONf_dihedral_angle_d12.4233782
X-RAY DIFFRACTIONf_chiral_restr0.0351107
X-RAY DIFFRACTIONf_plane_restr0.0031060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.22410.34961310.34872428X-RAY DIFFRACTION97
3.2241-3.37080.34941280.31472494X-RAY DIFFRACTION99
3.3708-3.54840.35741310.28492517X-RAY DIFFRACTION99
3.5484-3.77050.28971530.26562514X-RAY DIFFRACTION99
3.7705-4.06140.2531410.24872457X-RAY DIFFRACTION99
4.0614-4.46960.27211280.23142497X-RAY DIFFRACTION99
4.4696-5.11510.25841490.20762505X-RAY DIFFRACTION99
5.1151-6.43980.28271200.25162507X-RAY DIFFRACTION99
6.4398-39.08480.20541380.19652503X-RAY DIFFRACTION97

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