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- PDB-2zzt: Crystal structure of the cytosolic domain of the cation diffusion... -

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Basic information

Entry
Database: PDB / ID: 2zzt
TitleCrystal structure of the cytosolic domain of the cation diffusion facilitator family protein
ComponentsPutative uncharacterized protein
KeywordsTRANSPORT PROTEIN / cation diffusion facilitator (CDF) / transporter / zinc / membrane protein / cytosolic domain
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 / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / 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 / MAD / Resolution: 2.842 Å
AuthorsHiguchi, T. / Hattori, M. / Tanaka, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein
Authors: Higuchi, T. / Hattori, M. / Tanaka, Y. / Ishitani, R. / Nureki, O.
History
DepositionFeb 25, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2403
Polymers13,0481
Non-polymers1922
Water181
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4806
Polymers26,0962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area1430 Å2
ΔGint-42 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.719, 97.719, 83.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1-

SO4

21A-2-

SO4

31A-2-

SO4

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Components

#1: Protein Putative uncharacterized protein / cation diffusion facilitator


Mass: 13048.062 Da / Num. of mol.: 1 / Fragment: cytosolic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MS8 / Gene: CDF / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9WZX9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.94 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6-2.0M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97923, 0.97939, 0.96416
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979391
30.964161
ReflectionResolution: 2.84→50 Å / Num. obs: 3707 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 93.19 Å2 / Rsym value: 0.083 / Net I/σ(I): 32.5
Reflection shellResolution: 2.84→2.89 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.284 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.842→29.863 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.751 / SU ML: 0.51 / σ(F): 2.26 / Phase error: 30.86 / Stereochemistry target values: ML
Details: The F(+) AND F(-) were used for the refinement. Thus, the total nuber of the reflection is 6611.
RfactorNum. reflection% reflection
Rfree0.257 296 4.48 %
Rwork0.235 --
obs0.236 3707 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.016 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 133.7 Å2 / Biso mean: 87.821 Å2 / Biso min: 61.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.255 Å2-0 Å20 Å2
2---9.255 Å2-0 Å2
3---13.838 Å2
Refinement stepCycle: LAST / Resolution: 2.842→29.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 10 1 669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014684
X-RAY DIFFRACTIONf_angle_d1.475901
X-RAY DIFFRACTIONf_chiral_restr0.087104
X-RAY DIFFRACTIONf_plane_restr0.004117
X-RAY DIFFRACTIONf_dihedral_angle_d20.696248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.842-2.890.3291670.2783274344199
3.579-29.8650.2331290.2223041317090

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