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- PDB-7pgf: Calcium-selective Sp1 channel pore domain only -

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Basic information

Entry
Database: PDB / ID: 7pgf
TitleCalcium-selective Sp1 channel pore domain only
ComponentsIon transporter
KeywordsMEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex
Function / homologyHelix Hairpins - #70 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsLolicato, M. / Arrigoni, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ion transporter
D: Ion transporter


Theoretical massNumber of molelcules
Total (without water)31,0262
Polymers31,0262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.682, 133.682, 130.744
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'C' and ((resid 121 through 123 and (name N...
221(chain 'D' and (resid 121 through 132 or (resid 134...

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.754624, 0.42171, 0.502697), (0.442207, 0.239151, -0.864442), (-0.484764, 0.874624, -0.006014)-38.151619, 68.417992, -55.393169

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Components

#1: Protein Ion transporter


Mass: 15512.957 Da / Num. of mol.: 2 / Mutation: E56D, S57D, M60D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Gene: HW563_01415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y7EFG5

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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: 5.43 Å3/Da / Density % sol: 77.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: CaVSp1p purified in DM was concentrated to 13 mg mL-1 and reconstituted in bicelles prior crystallization to a final bicelle concentration of 8%. Native crystals grew in 25% PEG4000, 200 mM ...Details: CaVSp1p purified in DM was concentrated to 13 mg mL-1 and reconstituted in bicelles prior crystallization to a final bicelle concentration of 8%. Native crystals grew in 25% PEG4000, 200 mM MgCl2, 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 9000 / % possible obs: 97.17 % / Redundancy: 11.5 % / Biso Wilson estimate: 139.32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.2
Reflection shellResolution: 3.5→3.622 Å / Rmerge(I) obs: 1 / Num. unique obs: 879 / CC1/2: 0.126

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Processing

Software
NameVersionClassification
REFMAC5.8.0refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 3.5→14.93 Å / SU ML: 0.5953 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 423 4.7 %RANDOM
Rwork0.2646 8577 --
obs0.2658 9000 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.64 Å2
Refinement stepCycle: LAST / Resolution: 3.5→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 0 0 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012080
X-RAY DIFFRACTIONf_angle_d1.44872841
X-RAY DIFFRACTIONf_chiral_restr0.0756337
X-RAY DIFFRACTIONf_plane_restr0.0119357
X-RAY DIFFRACTIONf_dihedral_angle_d8.1736279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-40.42221450.37872786X-RAY DIFFRACTION99.97
4-5.010.32931390.27562827X-RAY DIFFRACTION99.93
5.01-14.930.23371390.23332964X-RAY DIFFRACTION99.68

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