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- PDB-6pgi: Asymmetric functions of a binuclear metal cluster within the tran... -

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Basic information

Entry
Database: PDB / ID: 6pgi
TitleAsymmetric functions of a binuclear metal cluster within the transport pathway of the ZIP transition metal transporters
ComponentsBbZIP
KeywordsTRANSPORT PROTEIN / ZIP / Zinc / Metal transporter / Cadmium / binuclear metal cluster
Function / homologyZinc/iron permease / ZIP Zinc transporter / metal ion transmembrane transporter activity / zinc ion transport / plasma membrane / : / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZhang, T. / Sui, D. / Zhang, C. / Logan, T. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129004 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115373 United States
CitationJournal: Faseb J. / Year: 2020
Title: Asymmetric functions of a binuclear metal center within the transport pathway of a human zinc transporter ZIP4.
Authors: Zhang, T. / Sui, D. / Zhang, C. / Cole, L. / Hu, J.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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

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Assembly

Deposited unit
A: BbZIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0893
Polymers30,8641
Non-polymers2252
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.782, 61.274, 54.753
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BbZIP


Mass: 30864.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB2405 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A0H3LM39
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 294.15 K / Method: lipidic cubic phase
Details: 33% (w/v) PEG 400, 100 mM NaCl, 100 mM CdCl2, 100 mM Tris-HCl (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 310 / % possible obs: 97.6 % / Redundancy: 3.9 % / Net I/σ(I): 6.9
Reflection shellResolution: 3.5→3.63 Å / Num. unique obs: 177225

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSA
Resolution: 3.5→40 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 36.38
RfactorNum. reflection% reflection
Rfree0.3203 370 9.55 %
Rwork0.2709 --
obs0.275 3874 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 2 0 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031532
X-RAY DIFFRACTIONf_angle_d0.5212082
X-RAY DIFFRACTIONf_dihedral_angle_d8.78881
X-RAY DIFFRACTIONf_chiral_restr0.034278
X-RAY DIFFRACTIONf_plane_restr0.003257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4831-3.98640.32711330.28951146X-RAY DIFFRACTION96
3.9864-5.01970.33681260.27971131X-RAY DIFFRACTION96
5.0197-33.45610.30221110.25811227X-RAY DIFFRACTION99

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