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- PDB-6iu3: Crystal structure of iron transporter VIT1 with zinc ions -

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Basic information

Entry
Database: PDB / ID: 6iu3
TitleCrystal structure of iron transporter VIT1 with zinc ions
ComponentsVIT1
KeywordsMETAL TRANSPORT / membrane protein
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciesEucalyptus grandis (rose gum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 20, 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
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)25,5135
Polymers24,9601
Non-polymers5534
Water00
1
A: VIT1
hetero molecules

A: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,02610
Polymers49,9202
Non-polymers1,1068
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4310 Å2
ΔGint-226 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.900, 290.240, 45.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 3.13 Å3/Da / Density % sol: 60.66 %
Description: The entry contains friedel pairs in I_plus/minus columns
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 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 26, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7001→48.375 Å / Num. obs: 16510 / % possible obs: 99.6154 % / Observed criterion σ(I): -3 / Redundancy: 12.782 % / Biso Wilson estimate: 74.36 Å2 / CC1/2: 0.9975 / Rmerge(I) obs: 0.1134 / Net I/σ(I): 14.5139 / Num. measured all: 115869
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Net I/σ(I) obs
5.8142-48.382799.101813.08660.0575129959930.996441.4791
4.616-5.814299.678113.9290.0689129409290.999332.112
4.0329-4.61697.837813.67180.106123739050.997926.4377
3.6643-4.032910012.17560.1496109589000.994515.0151
3.4017-3.664310011.82510.2436107499090.98739.2944
3.2012-3.401710011.27390.3875101248980.97515.6743
3.0409-3.201210012.42920.5424109758830.97313.9096
2.9086-3.040910012.83770.7088113108810.96373.0327
2.7966-2.908699.665613.10180.9458117138940.93132.2529
2.7001-2.796610013.43871.3778117328730.89771.6334

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.373 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.13 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.305 1643 9.95 %
Rwork0.2768 14867 -
obs0.2796 16510 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 425.4 Å2 / Biso mean: 114.0346 Å2 / Biso min: 43.01 Å2
Refinement stepCycle: final / Resolution: 2.7→48.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 25 0 1556
Biso mean--141.48 --
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.77950.41731310.32471210134199
2.7795-2.86920.3831400.34141247138799
2.8692-2.97170.38911330.33621220135399
2.9717-3.09070.45321330.327512791412100
3.0907-3.23130.38971330.33551219135299
3.2313-3.40160.36931380.326312451383100
3.4016-3.61470.33661440.342312481392100
3.6147-3.89370.37671370.302412471384100
3.8937-4.28530.37411410.26812481389100
4.2853-4.90490.23771330.24361196132997
4.9049-6.17760.31291420.292712531395100
6.1776-48.38110.21281380.220512551393100

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