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- PDB-6iu4: Crystal structure of iron transporter VIT1 with cobalt ion -

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Basic information

Entry
Database: PDB / ID: 6iu4
TitleCrystal structure of iron transporter VIT1 with cobalt ion
ComponentsVIT1
KeywordsMETAL TRANSPORT / membrane protein
Function / homology:
Function and homology information
Biological speciesEucalyptus grandis (rose gum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKato, T. / Nishizawa, T. / Yamashita, K. / Taniguchi, R. / Kumazaki, K. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Plants / Year: 2019
Title: Crystal structure of plant vacuolar iron transporter VIT1.
Authors: Kato, T. / Kumazaki, K. / Wada, M. / Taniguchi, R. / Nakane, T. / Yamashita, K. / Hirata, K. / Ishitani, R. / Ito, K. / Nishizawa, T. / Nureki, O.
History
DepositionNov 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2155
Polymers24,9601
Non-polymers2554
Water0
1
A: VIT1
hetero molecules

A: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,43010
Polymers49,9202
Non-polymers5108
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4420 Å2
ΔGint-229 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.830, 290.770, 45.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

CO

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Components

#1: Protein VIT1


Mass: 24960.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eucalyptus grandis (rose gum) / Plasmid: modified pYES2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): modified BY4742
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co

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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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 24-26% PEG 500DME, 0.1 M HEPES pH7.0, 0.25-30 M ammonium sulfate, 0.0004 M zinc cloride, 0.2 M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.5→43.571 Å / Num. obs: 7416 / % possible obs: 99.1 % / Redundancy: 6.029 % / Biso Wilson estimate: 92.05 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.51 / Rrim(I) all: 0.554 / Χ2: 0.829 / Net I/σ(I): 2.86 / Num. measured all: 25496 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.715.8746.5250.8937896516450.5117.08699.1
3.71-3.976.1972.0841.3438986366290.6592.25998.9
3.97-4.296.3660.6582.0338136045990.7930.71399.2
4.29-4.76.1810.5872.8733875525480.8090.63599.3
4.7-5.256.2460.4423.0930424894870.9350.47699.6
5.25-6.065.8570.392.9125834434410.9280.42399.5
6.06-7.425.4140.3153.920793863840.9460.3599.5
7.42-10.56.110.216.5618823103080.9670.23299.4
10.5-43.5715.4410.1378.2710231961880.9850.15195.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→43.571 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 36.84
RfactorNum. reflection% reflection
Rfree0.3556 748 10.09 %
Rwork0.3061 --
obs0.311 7416 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.4 Å2 / Biso mean: 86.1169 Å2 / Biso min: 33.7 Å2
Refinement stepCycle: final / Resolution: 3.5→43.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 4 0 1466
Biso mean--200.68 --
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5002-3.77030.40741490.35011317146697
3.7703-4.14940.34061490.34411325147497
4.1494-4.74920.37071490.3071338148798
4.7492-5.98110.38831490.32281352150198
5.9811-43.57420.31591520.26311336148897

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