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- PDB-6iu9: Crystal structure of cytoplasmic metal binding domain with iron ions -

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Basic information

Entry
Database: PDB / ID: 6iu9
TitleCrystal structure of cytoplasmic metal binding domain with iron ions
ComponentsVIT1
KeywordsMETAL TRANSPORT / membrane protein
Function / homology:
Function and homology information
Biological speciesEucalyptus grandis (rose gum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKato, T. / Nishizawa, T. / Yamashita, K. / 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 / Category: citation_author
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn_type.id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIT1
B: VIT1
C: VIT1
D: VIT1
E: VIT1
F: VIT1
H: VIT1
I: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,55035
Polymers72,8508
Non-polymers1,69927
Water1448
1
A: VIT1
B: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,91313
Polymers18,2132
Non-polymers70011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-164 kcal/mol
Surface area9070 Å2
MethodPISA
2
C: VIT1
D: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3905
Polymers18,2132
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-165 kcal/mol
Surface area9110 Å2
MethodPISA
3
E: VIT1
F: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,71710
Polymers18,2132
Non-polymers5048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-136 kcal/mol
Surface area9410 Å2
MethodPISA
4
H: VIT1
I: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5307
Polymers18,2132
Non-polymers3175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-195 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.321, 85.321, 97.573
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
VIT1


Mass: 9106.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eucalyptus grandis (rose gum) / Plasmid: modified pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.81 Å3/Da / Density % sol: 56.3 % / Mosaicity: 0.11 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21-23% PEG600, 0.1 M HEPES pH7.0 and 0.001-0.003 M zinc cloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.563
11K, H, -L20.437
ReflectionResolution: 3→42.6607 Å / Num. obs: 15910 / % possible obs: 99.9937 % / Redundancy: 5.139 % / CC1/2: 0.9848 / Rmerge(I) obs: 0.2096 / Rpim(I) all: 0.1035 / Rrim(I) all: 0.2342 / Net I/σ(I): 5.9655 / Num. measured all: 81761
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Net I/σ(I) obs
6.4568-42.6651005.20030.1173823215830.98399.5701
5.1277-6.45681005.32870.1663846215880.95758.9143
4.4803-5.12771005.17820.186822315880.94528.6004
4.071-4.48031005.30420.2183849216010.93017.8851
3.7794-4.0711005.13310.2694817715930.90916.7108
3.5567-3.77941005.04150.3471801615900.8695.748
3.3787-3.55671005.2350.4901835515960.84224.8644
3.2317-3.37871005.06590.9786799915790.43073.4694
3.1073-3.23171004.94652.1999794916070.2652.2498
3-3.107399.93694.95653.3153785615850.09871.6638

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU5

6iu5


Resolution: 3→42.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.075 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 718 4.5 %RANDOM
Rwork0.1916 ---
obs0.1947 15192 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 234.97 Å2 / Biso mean: 94.125 Å2 / Biso min: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.68 Å2-0 Å2-0 Å2
2---9.68 Å2-0 Å2
3---19.37 Å2
Refinement stepCycle: final / Resolution: 3→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 27 8 4751
Biso mean--100.53 50.48 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174469
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6556503
X-RAY DIFFRACTIONr_angle_other_deg1.2281.58110390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84622.517294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04315854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9931539
X-RAY DIFFRACTIONr_chiral_restr0.0680.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02990
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.635 48 -
Rwork0.476 1150 -
all-1198 -
obs--99.58 %

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