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

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Basic information

Entry
Database: PDB / ID: 5tsa
TitleCrystal structure of the Zrt-/Irt-like protein from Bordetella bronchiseptica with bound Zn2+
ComponentsMembrane protein
KeywordsMETAL BINDING PROTEIN / ZIP / transporter / zinc / cadmium / lipidic cubic phase / binuclear metal centerzinc
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 / molecular replacement / Resolution: 2.4 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)31,5148
Polymers31,0091
Non-polymers5057
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-190 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.006, 61.073, 94.394
Angle α, β, γ (deg.)90.000, 104.020, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Membrane protein /


Mass: 31009.291 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.48 Å3/Da / Density % sol: 50.41 % / Mosaicity: 0.1 °
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: 23-ID-D / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 2.4→33.373 Å / Num. obs: 11734 / % possible obs: 97.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 11.7 / Num. measured all: 80183
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.4970.8290.819193.6
8.96-41.916.20.0550.998197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.89 Å33.37 Å
Translation5.89 Å33.37 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TBA

Resolution: 2.4→33.373 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.09
RfactorNum. reflection% reflection
Rfree0.2571 582 4.99 %
Rwork0.2122 --
obs0.2143 11734 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.19 Å2 / Biso mean: 46.319 Å2 / Biso min: 24.33 Å2
Refinement stepCycle: final / Resolution: 2.4→33.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 7 11 1593
Biso mean--67.62 44.9 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081623
X-RAY DIFFRACTIONf_angle_d0.9652180
X-RAY DIFFRACTIONf_chiral_restr0.046282
X-RAY DIFFRACTIONf_plane_restr0.005271
X-RAY DIFFRACTIONf_dihedral_angle_d13.853518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3958-2.50480.25741140.26092625273993
2.5048-2.63680.31211440.24852680282497
2.6368-2.80190.3071680.22292663283197
2.8019-3.01810.29171780.21822675285397
3.0181-3.32160.2671220.21012730285298
3.3216-3.80160.22171640.20242701286598
3.8016-4.78740.24021300.19982759288998
4.7874-33.37610.24411150.20712768288398

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