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- PDB-6vd9: Metal-bound C-terminal domain of the CzcD transporter from Cupriv... -

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Basic information

Entry
Database: PDB / ID: 6vd9
TitleMetal-bound C-terminal domain of the CzcD transporter from Cuprividus metallidurans
ComponentsMetal cation efflux system protein CzcD
KeywordsTRANSPORT PROTEIN / cation diffusion facilitator protein (CDF) / CzcD
Function / homology
Function and homology information


detoxification of zinc ion / zinc ion transport / monoatomic cation transmembrane transporter activity / response to cadmium ion / plasma membrane
Similarity search - Function
: / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
NICKEL (II) ION / Metal cation efflux system protein CzcD
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metal cation efflux system protein CzcD
B: Metal cation efflux system protein CzcD
C: Metal cation efflux system protein CzcD
D: Metal cation efflux system protein CzcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6858
Polymers33,4504
Non-polymers2354
Water4,107228
1
A: Metal cation efflux system protein CzcD
C: Metal cation efflux system protein CzcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8424
Polymers16,7252
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metal cation efflux system protein CzcD
D: Metal cation efflux system protein CzcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8424
Polymers16,7252
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.760, 39.029, 63.965
Angle α, β, γ (deg.)98.78, 104.76, 90.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Metal cation efflux system protein CzcD / Cobalt-zinc-cadmium resistance protein CzcD


Mass: 8362.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria)
Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: czcD, Rmet_5979 / Production host: Escherichia coli (E. coli) / References: UniProt: P13512
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.7, 22% (w/v) PEG 3350

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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 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→39 Å / Num. obs: 29396 / % possible obs: 96.3 % / Redundancy: 2.9 % / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1610 / CC1/2: 0.932

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Processing

Software
NameVersionClassification
XDS5.8.0238data reduction
Aimlessdata scaling
MOLREPphasing
REFMAC7.0.073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VD8

6vd8


Resolution: 1.75→38.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.907 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25808 1453 4.9 %RANDOM
Rwork0.2236 ---
obs0.2253 27942 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0.31 Å20.2 Å2
2--0.22 Å2-0.33 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.75→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 4 228 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172153
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6263111
X-RAY DIFFRACTIONr_angle_other_deg1.3631.575004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21626.45896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
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_it2.1612.3681132
X-RAY DIFFRACTIONr_mcbond_other2.162.3671131
X-RAY DIFFRACTIONr_mcangle_it3.1353.5291406
X-RAY DIFFRACTIONr_mcangle_other3.1343.531407
X-RAY DIFFRACTIONr_scbond_it2.9852.6351142
X-RAY DIFFRACTIONr_scbond_other2.9712.6361142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3533.8481702
X-RAY DIFFRACTIONr_long_range_B_refined6.41230.132546
X-RAY DIFFRACTIONr_long_range_B_other6.37129.8232496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 123 -
Rwork0.212 2047 -
obs--95.22 %

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