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- PDB-3cij: Crystal structure of A. fulgidus periplasmic binding protein ModA... -

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Basic information

Entry
Database: PDB / ID: 3cij
TitleCrystal structure of A. fulgidus periplasmic binding protein ModA/WtpA with bound tungstate
ComponentsUPF0100 protein AF_0094
KeywordsTRANSPORT PROTEIN / archaeal periplasmic binding protein / UNKNOWN FUNCTION / METAL BINDING PROTEIN
Function / homology
Function and homology information


tungstate binding / metal ion binding / plasma membrane
Similarity search - Function
Tungstate ABC transporter, substrate-binding protein WtpA / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Molybdate/tungstate-binding protein WtpA
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.07 Å
AuthorsComellas-Bigler, M. / Hollenstein, K. / Locher, K.P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2009
Title: Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins.
Authors: Hollenstein, K. / Comellas-Bigler, M. / Bevers, L.E. / Feiters, M.C. / Meyer-Klaucke, W. / Hagedoorn, P.L. / Locher, K.P.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: UPF0100 protein AF_0094
B: UPF0100 protein AF_0094
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1255
Polymers67,5332
Non-polymers5923
Water14,844824
1
A: UPF0100 protein AF_0094
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0142
Polymers33,7671
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0100 protein AF_0094
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1103
Polymers33,7671
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.901, 75.396, 116.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0100 protein AF_0094


Mass: 33766.504 Da / Num. of mol.: 2 / Fragment: residues 33-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: ModA = AF0094 / Production host: Escherichia coli (E. coli) / References: UniProt: O30142
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 30mM Tris pH 8.4, 0.16M Na2SO4, 5% glycerol, 28% PEG 4K, sitting drop at 293K. , VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorDate: Mar 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.07→30 Å / Num. obs: 285208

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.004data extraction
SHELXLrefinement
RefinementResolution: 1.07→10 Å
RfactorNum. reflection
Rfree0.1493 14081
all0.1264 -
obs-270746
Displacement parametersBiso mean: 19.844 Å2
Refinement stepCycle: LAST / Resolution: 1.07→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4827 0 15 824 5666

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