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- PDB-6nq7: Crystal structure of YetJ from Bacillus Subtilis crystallized in ... -

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Basic information

Entry
Database: PDB / ID: 6nq7
TitleCrystal structure of YetJ from Bacillus Subtilis crystallized in lipidic cubic phase
ComponentsUncharacterized protein YetJ
KeywordsMEMBRANE PROTEIN / Ca2+ channel structure / closed state / pH sensor
Function / homologyBax inhibitor 1-related / Inhibitor of apoptosis-promoting Bax1 / regulation of proteolysis / calcium channel activity / calcium ion transport / membrane / plasma membrane / GADOLINIUM ATOM / pH-sensitive calcium channel
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YetJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4712
Polymers23,3141
Non-polymers1571
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.864, 63.037, 47.336
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein YetJ


Mass: 23313.910 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 8
Details: 0.1 M Tris, pH 7.8, 5% PGA-LM (w/v), and 30% PEG 400 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→47.22 Å / Num. obs: 6634 / % possible obs: 95.3 % / Redundancy: 7 % / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.63 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PGR

4pgr


Resolution: 2.5→47.22 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.076 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26025 343 5.2 %RANDOM
Rwork0.24258 ---
obs0.24347 6273 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å2-1.28 Å2
2--1.37 Å20 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 1 31 1624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021647
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9622223
X-RAY DIFFRACTIONr_angle_other_deg0.88333740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9985203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7712255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14715262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.207155
X-RAY DIFFRACTIONr_chiral_restr0.0580.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0223.867815
X-RAY DIFFRACTIONr_mcbond_other1.0213.864814
X-RAY DIFFRACTIONr_mcangle_it1.7755.7961017
X-RAY DIFFRACTIONr_mcangle_other1.7745.7991018
X-RAY DIFFRACTIONr_scbond_it1.0284.008820
X-RAY DIFFRACTIONr_scbond_other1.0274.007821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7315.9531207
X-RAY DIFFRACTIONr_long_range_B_refined3.44631.6381901
X-RAY DIFFRACTIONr_long_range_B_other3.39931.5641895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 19 -
Rwork0.263 360 -
obs--73.03 %

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