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- PDB-6vda: Metal-bound C-terminal domain of CzcD transporter from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 6vda
TitleMetal-bound C-terminal domain of CzcD transporter from Thermotoga maritima
ComponentsZT_dimer domain-containing protein
KeywordsTRANSPORT PROTEIN / cation diffusion facilitator protein (CDF) / CzcD
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / metal ion binding / membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cation efflux protein cytoplasmic domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMaher, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT180100397 Australia
CitationJournal: J.Inorg.Biochem. / Year: 2020
Title: Structural and functional characterizations of the C-terminal domains of CzcD proteins.
Authors: Udagedara, S.R. / La Porta, D.M. / Spehar, C. / Purohit, G. / Hein, M.J.A. / Fatmous, M.E. / Casas Garcia, G.P. / Ganio, K. / McDevitt, C.A. / Maher, M.J.
History
DepositionDec 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZT_dimer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1954
Polymers11,9381
Non-polymers2583
Water1267
1
A: ZT_dimer domain-containing protein
hetero molecules

A: ZT_dimer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3918
Polymers23,8762
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area1580 Å2
ΔGint-49 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.420, 97.420, 84.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ZT_dimer domain-containing protein


Mass: 11937.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M-2.0 M ammonium sulfate, 1.0 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→49 Å / Num. obs: 6149 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.992 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 641 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
XDS5.8.0258data reduction
Aimlessdata scaling
MOLREPphasing
REFMAC7.0.078refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZT

2zzt


Resolution: 2.4→48.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.31 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28352 618 10.5 %RANDOM
Rwork0.2339 ---
obs0.23902 5289 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 11 7 707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013715
X-RAY DIFFRACTIONr_bond_other_d0.0010.017658
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.646968
X-RAY DIFFRACTIONr_angle_other_deg1.1221.5841515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.057587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84321.59144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00215129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.212157
X-RAY DIFFRACTIONr_chiral_restr0.0410.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4086.955345
X-RAY DIFFRACTIONr_mcbond_other2.4056.948344
X-RAY DIFFRACTIONr_mcangle_it3.60510.425430
X-RAY DIFFRACTIONr_mcangle_other3.60110.434431
X-RAY DIFFRACTIONr_scbond_it2.3237.277370
X-RAY DIFFRACTIONr_scbond_other2.3117.263360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.74510.805525
X-RAY DIFFRACTIONr_long_range_B_refined5.85879.472724
X-RAY DIFFRACTIONr_long_range_B_other5.8779.346722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 27 -
Rwork0.305 267 -
obs--65.48 %
Refinement TLS params.Method: refined / Origin x: 0.9913 Å / Origin y: 16.534 Å / Origin z: 31.6611 Å
111213212223313233
T0.117 Å20.0055 Å2-0.0762 Å2-0.0389 Å2-0.0275 Å2--0.1083 Å2
L4.0984 °22.3143 °2-0.0632 °2-5.3086 °2-0.4929 °2--4.4387 °2
S0.111 Å °0.0775 Å °0.2564 Å °0.0654 Å °0.013 Å °0.1094 Å °0.4803 Å °-0.2773 Å °-0.1241 Å °

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