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- PDB-5my5: Tungstate binding protein - TupA - from Desulfovibrio alaskensis G20 -

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Basic information

Entry
Database: PDB / ID: 5my5
TitleTungstate binding protein - TupA - from Desulfovibrio alaskensis G20
ComponentsABC transporter periplasmic substrate-binding protein
KeywordsTRANSPORT PROTEIN / susbtrate binding protein / TupA / tungstate / Desulfovibrio alaskensis G20 / ABC transporter / tungsten detection / sulphate reducing bacteria
Function / homology: / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ABC transporter periplasmic substrate-binding protein
Function and homology information
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOtrelo-Cardoso, A.R. / Correia, M.A.S.C. / Santos-Silva, T.
Funding support Portugal, 3items
OrganizationGrant numberCountry
FCT/MCTESEXPL/BBB-BEP/0274/2012 Portugal
FCT/MCTESPTDC/QEQ-MED/1902/2014 Portugal
FCT/MCTESSFRH/BD/85806/2012 Portugal
Citation
Journal: Sci Rep / Year: 2017
Title: Highly selective tungstate transporter protein TupA from Desulfovibrio alaskensis G20.
Authors: Otrelo-Cardoso, A.R. / Nair, R.R. / Correia, M.A.S. / Cordeiro, R.S.C. / Panjkovich, A. / Svergun, D.I. / Santos-Silva, T. / Rivas, M.G.
#1: Journal: Int J Mol Sci / Year: 2014
Title: TupA: a tungstate binding protein in the periplasm of Desulfovibrio alaskensis G20.
Authors: Otrelo-Cardoso, A.R. / Nair, R.R. / Correia, M.A.S. / Rivas, M.G. / Santos-Silva, T.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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.ptnr2_auth_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7924
Polymers29,6981
Non-polymers943
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-21 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.323, 42.530, 54.753
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter periplasmic substrate-binding protein


Mass: 29697.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (strain G20) (bacteria)
Gene: Dde_0234 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q316W1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M HEPES (pH 7.5) and 30% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.4→42.53 Å / Num. obs: 46519 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.033 / Rrim(I) all: 0.048 / Net I/σ(I): 12.8
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2277 / CC1/2: 0.903 / Rpim(I) all: 0.288 / Rrim(I) all: 0.414

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LR1, 3MUQ

3lr1

3muq


Resolution: 1.4→42.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.722 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21748 2257 4.9 %RANDOM
Rwork0.17605 ---
obs0.17812 44239 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.668 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å2-1.13 Å2
2---0.38 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.4→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 3 332 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021933
X-RAY DIFFRACTIONr_bond_other_d0.0020.021823
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9662626
X-RAY DIFFRACTIONr_angle_other_deg1.05534250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77825.67674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.314155
X-RAY DIFFRACTIONr_chiral_restr0.1330.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02356
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_it2.0162.1011003
X-RAY DIFFRACTIONr_mcbond_other2.012.0981002
X-RAY DIFFRACTIONr_mcangle_it2.7133.1451253
X-RAY DIFFRACTIONr_mcangle_other2.7173.1481254
X-RAY DIFFRACTIONr_scbond_it3.0362.384930
X-RAY DIFFRACTIONr_scbond_other3.0062.374927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4073.4371370
X-RAY DIFFRACTIONr_long_range_B_refined5.72727.3262291
X-RAY DIFFRACTIONr_long_range_B_other5.61526.3752208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 158 -
Rwork0.298 3261 -
obs--98.3 %

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