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- PDB-5tsb: Crystal structure of the Zrt-/Irt-like protein from Bordetella br... -

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Basic information

Entry
Database: PDB / ID: 5tsb
TitleCrystal structure of the Zrt-/Irt-like protein from Bordetella bronchiseptica with bound Cd2+
ComponentsMembrane protein
KeywordsMETAL BINDING PROTEIN / ZIP / transporter / zinc / cadmium / lipidic cubic phase / binuclear metal center / membrane protein
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 / SAD / Resolution: 2.7 Å
AuthorsZhang, T. / Fellner, M. / Sui, D. / Liu, J. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115373 United States
CitationJournal: Sci Adv / Year: 2017
Title: Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway.
Authors: Zhang, T. / Liu, J. / Fellner, M. / Zhang, C. / Sui, D. / Hu, J.
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0695
Polymers31,6191
Non-polymers4504
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-60 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.076, 61.596, 54.870
Angle α, β, γ (deg.)90.000, 108.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Membrane protein


Mass: 31618.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) (bacteria)
Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Plasmid: pLW01 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) pLysS / References: UniProt: A0A0H3LM39
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.39 % / Mosaicity: 0.529 °
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 7.5
Details: protein concentration: 15 mg/mL; buffer: 10 mM Hepes pH 7.3, 300 mM NaCl, 5% Glycerol, 0.02% DDM; crystallization condition: 0.1 M Sodium chloride, 0.1 M Cadmium chloride hemi, 0.1 M Tris-HCl pH 7.5, 33% PEG 400

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→26.494 Å / Num. obs: 7889 / % possible obs: 93.2 % / Redundancy: 10.1 % / Biso Wilson estimate: 53.74 Å2 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.048 / Rrim(I) all: 0.169 / Χ2: 1.132 / Net I/av σ(I): 17.4 / Net I/σ(I): 4.6 / Num. measured all: 79447
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.84.20.4820.896183.3
2.8-2.915.50.4520.904191.1
2.91-3.046.90.4320.953196.5
3.04-3.290.4090.961196.8
3.2-3.410.80.3540.976196.2
3.4-3.6611.30.2680.985185.9
3.66-4.0312.90.1940.994196.8
4.03-4.6212.70.1460.994198
4.62-5.8113.50.1310.996195.5
5.81-5012.70.10.998191.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→26.494 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.2675 395 5.03 %
Rwork0.2265 --
obs0.2286 7857 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.17 Å2 / Biso mean: 48.1683 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 2.7→26.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 3 6 1508
Biso mean--81.72 38.69 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111539
X-RAY DIFFRACTIONf_angle_d1.2092070
X-RAY DIFFRACTIONf_chiral_restr0.064271
X-RAY DIFFRACTIONf_plane_restr0.007257
X-RAY DIFFRACTIONf_dihedral_angle_d13.864495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6958-2.90370.29791360.2582510264681
2.9037-3.19550.23081480.22672989313795
3.1955-3.65680.27811620.21522809297191
3.6568-4.60330.26431570.20773022317997
4.6033-26.4950.26881480.2422863301191

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