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- PDB-6iu8: Crystal structure of cytoplasmic metal binding domain with cobalt ions -

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Basic information

Entry
Database: PDB / ID: 6iu8
TitleCrystal structure of cytoplasmic metal binding domain with cobalt ions
ComponentsVIT1
KeywordsMETAL TRANSPORT / membrane protein
Function / homology:
Function and homology information
Biological speciesEucalyptus grandis (rose gum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Nov 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
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_asym_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.ptnr2_symmetry / _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.pdbx_dist_value / _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.ptnr2_symmetry

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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)74,89241
Polymers72,8508
Non-polymers2,04233
Water1448
1
A: VIT1
B: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,71010
Polymers18,2132
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-154 kcal/mol
Surface area9210 Å2
MethodPISA
2
C: VIT1
D: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,76911
Polymers18,2132
Non-polymers5569
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-160 kcal/mol
Surface area9020 Å2
MethodPISA
3
E: VIT1
F: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,70410
Polymers18,2132
Non-polymers4918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-143 kcal/mol
Surface area9290 Å2
MethodPISA
4
H: VIT1
I: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,71010
Polymers18,2132
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-155 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.503, 85.503, 98.355
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.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.85 Å3/Da / Density % sol: 56.83 % / Mosaicity: 0.16 °
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: 1.605 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.605 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.609
11K, H, -L20.391
ReflectionResolution: 2.7→19.72 Å / Num. obs: 22053 / % possible obs: 99.7 % / Redundancy: 10.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.042 / Rrim(I) all: 0.138 / Net I/σ(I): 11.2 / Num. measured all: 230049 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1 / Redundancy: 10.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.830.743112629650.7610.2390.7783100
8.96-19.720.08258265550.9960.0270.0872390.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU5

6iu5


Resolution: 2.7→19.72 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.915 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 986 4.5 %RANDOM
Rwork0.1584 ---
obs0.1608 21040 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.96 Å2 / Biso mean: 66.018 Å2 / Biso min: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2--1.53 Å20 Å2
3----3.05 Å2
Refinement stepCycle: final / Resolution: 2.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 33 8 4757
Biso mean--67.58 41.45 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174469
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6556503
X-RAY DIFFRACTIONr_angle_other_deg1.221.58110390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22922.517294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95615854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9731539
X-RAY DIFFRACTIONr_chiral_restr0.0740.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02990
LS refinement shellResolution: 2.7→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 72 -
Rwork0.259 1582 -
all-1654 -
obs--99.88 %

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