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- PDB-6iu6: Crystal structure of cytoplasmic metal binding domain with nickel ions -

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Basic information

Entry
Database: PDB / ID: 6iu6
TitleCrystal structure of cytoplasmic metal binding domain with nickel ions
ComponentsVIT1
KeywordsMETAL TRANSPORT / membrane protein
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesEucalyptus grandis (rose gum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
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)74,92742
Polymers72,8508
Non-polymers2,07634
Water1448
1
A: VIT1
B: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,08116
Polymers18,2132
Non-polymers86914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-164 kcal/mol
Surface area9110 Å2
MethodPISA
2
C: VIT1
D: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4476
Polymers18,2132
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-141 kcal/mol
Surface area8970 Å2
MethodPISA
3
E: VIT1
F: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,94414
Polymers18,2132
Non-polymers73112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-114 kcal/mol
Surface area9300 Å2
MethodPISA
4
H: VIT1
I: VIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4546
Polymers18,2132
Non-polymers2414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-135 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.744, 84.744, 97.398
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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Ni
#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: 2.77 Å3/Da / Density % sol: 55.62 % / 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: 1.485 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.485 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.753
11K, H, -L20.247
ReflectionResolution: 2.9→42.372 Å / Num. obs: 17355 / % possible obs: 99.9885 % / Redundancy: 5.1 % / CC1/2: 0.9918 / Rmerge(I) obs: 0.1259 / Rpim(I) all: 0.061 / Rrim(I) all: 0.14 / Net I/σ(I): 7.7505 / Num. measured all: 8962 / Scaling rejects: 625
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Net I/σ(I) obs
2.9-3.003999.8874.99490.306883117680.8873.4761
3.0039-3.12411005.10610.264890517440.90954.3071
3.1241-3.26621005.29110.2223918017350.94055.5521
3.2662-3.43841005.23170.1866892017050.95457.3127
3.4384-3.65371005.01450.1727867017290.95668.2265
3.6537-3.93561005.13590.1528892117370.96748.8726
3.9356-4.33131005.30020.1358918017320.97599.6405
4.3313-4.95721005.07410.1238890017540.97539.8846
4.9572-6.24241005.31320.123907517080.975710.0015
6.2424-42.37651005.1870.0984904117430.990210.3266

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU5

6iu5


Resolution: 2.9→42.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.808 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 798 4.6 %RANDOM
Rwork0.1448 ---
obs0.1477 16557 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.9 Å2 / Biso mean: 66.441 Å2 / Biso min: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.47 Å20 Å20 Å2
2--5.47 Å20 Å2
3----10.94 Å2
Refinement stepCycle: final / Resolution: 2.9→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 34 8 4758
Biso mean--71.08 44.65 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174469
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.6556503
X-RAY DIFFRACTIONr_angle_other_deg1.321.58110390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68922.517294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8915854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1511539
X-RAY DIFFRACTIONr_chiral_restr0.0830.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02990
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 72 -
Rwork0.223 1206 -
all-1278 -
obs--99.84 %

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