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- PDB-8czj: A bacteria Zrt/Irt-like protein in the apo state -

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Basic information

Entry
Database: PDB / ID: 8czj
TitleA bacteria Zrt/Irt-like protein in the apo state
ComponentsPutative membrane protein
KeywordsTRANSPORT PROTEIN
Function / homologyZinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / Chem-MPG / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.751 Å
AuthorsZhang, Y. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter.
Authors: Zhang, Y. / Jiang, Y. / Gao, K. / Sui, D. / Yu, P. / Su, M. / Wei, G.W. / Hu, J.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative membrane protein
B: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,99619
Polymers62,0192
Non-polymers3,97717
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-139 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.985, 117.661, 64.290
Angle α, β, γ (deg.)90.000, 104.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:54 or resseq 56:78 or (resid...
21(chain B and (resseq 5:54 or resseq 56:78 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL(chain A and (resseq 5:54 or resseq 56:78 or (resid...AA5 - 545 - 54
12VALVALLEULEU(chain A and (resseq 5:54 or resseq 56:78 or (resid...AA56 - 7856 - 78
13GLYGLYGLYGLY(chain A and (resseq 5:54 or resseq 56:78 or (resid...AA7979
14SERSERGLYGLY(chain A and (resseq 5:54 or resseq 56:78 or (resid...AA5 - 3095 - 309
15SERSERGLYGLY(chain A and (resseq 5:54 or resseq 56:78 or (resid...AA5 - 3095 - 309
21SERSERVALVAL(chain B and (resseq 5:54 or resseq 56:78 or (resid...BB5 - 545 - 54
22VALVALLEULEU(chain B and (resseq 5:54 or resseq 56:78 or (resid...BB56 - 7856 - 78
23GLYGLYGLYGLY(chain B and (resseq 5:54 or resseq 56:78 or (resid...BB7979
24SERSERGLYGLY(chain B and (resseq 5:54 or resseq 56:78 or (resid...BB5 - 3095 - 309
25SERSERGLYGLY(chain B and (resseq 5:54 or resseq 56:78 or (resid...BB5 - 3095 - 309

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Components

#1: Protein Putative membrane protein


Mass: 31009.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Strain: ATCC BAA-588 / NCTC 13252 / RB50 / Gene: BB2405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3LM39
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 6.5 / Details: 27%PEG200,0.02M NaAc 4.0,0.2M(NH4)2SO4,0.02M NaCl

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.751→37.109 Å / Num. obs: 22227 / % possible obs: 97.26 % / Redundancy: 3.6 % / Biso Wilson estimate: 62.63 Å2 / CC1/2: 0.772 / Rpim(I) all: 0.088 / Rrim(I) all: 0.194 / Χ2: 0.547 / Net I/σ(I): 6.7
Reflection shellResolution: 3.001→3.11 Å / Num. unique obs: 17721 / CC1/2: 0.851 / CC star: 0.959 / Rpim(I) all: 0.289

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSB

5tsb


Resolution: 2.751→37.109 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1997 8.98 %
Rwork0.2326 20230 -
obs0.2352 22227 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.71 Å2 / Biso mean: 55.0739 Å2 / Biso min: 27.8 Å2
Refinement stepCycle: final / Resolution: 2.751→37.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 263 7 4289
Biso mean--59.88 52.28 -
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014336
X-RAY DIFFRACTIONf_angle_d1.315865
X-RAY DIFFRACTIONf_chiral_restr0.069722
X-RAY DIFFRACTIONf_plane_restr0.008726
X-RAY DIFFRACTIONf_dihedral_angle_d13.7872498
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2392X-RAY DIFFRACTION9.15TORSIONAL
12B2392X-RAY DIFFRACTION9.15TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.751-2.81970.34711060.3303105669
2.8197-2.89590.33831270.336127183
2.8959-2.98110.33821370.3112141792
2.9811-3.07730.35141460.2832148898
3.0773-3.18720.33611560.2876151799
3.1872-3.31480.28231460.25881528100
3.3148-3.46550.28821510.2371531100
3.4655-3.64810.26091520.22491520100
3.6481-3.87640.24421470.21891556100
3.8764-4.17530.24241540.2211537100
4.1753-4.59480.29361180.2203119978
4.5948-5.25810.23521520.2207151899
5.2581-6.61850.27851470.2451541100

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