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- PDB-5teu: Brucella periplasmic binding protein YehZ -

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Basic information

Entry
Database: PDB / ID: 5teu
TitleBrucella periplasmic binding protein YehZ
ComponentsSubstrate-binding region of ABC-type glycine betaine transport system
KeywordsTRANSPORT PROTEIN / Brucella / periplasmic binding protein / general stress response / ABC transporter
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / metal ion binding
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / L(+)-TARTARIC ACID / Substrate-binding region of ABC-type glycine betaine transport system
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsHerrou, J. / Crosson, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI107792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107159 United States
CitationJournal: J. Bacteriol. / Year: 2017
Title: Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria.
Authors: Herrou, J. / Willett, J.W. / Czyz, D.M. / Babnigg, G. / Kim, Y. / Crosson, S.
History
DepositionSep 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Substrate-binding region of ABC-type glycine betaine transport system
B: Substrate-binding region of ABC-type glycine betaine transport system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,03811
Polymers64,1032
Non-polymers9369
Water12,791710
1
A: Substrate-binding region of ABC-type glycine betaine transport system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3934
Polymers32,0511
Non-polymers3423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Substrate-binding region of ABC-type glycine betaine transport system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6457
Polymers32,0511
Non-polymers5936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.370, 111.370, 122.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-641-

HOH

21B-816-

HOH

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Components

#1: Protein Substrate-binding region of ABC-type glycine betaine transport system


Mass: 32051.260 Da / Num. of mol.: 2 / Fragment: UNP residues 25-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: BAB1_0226 / Plasmid: pET28 / Details (production host): Kan resistant, N-ter His tag
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2YP76
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 3 Å3/Da / Density % sol: 59.1 % / Description: hexagonal rods
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 200 mM K/Na tartrate, 2.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.62→41.12 Å / Num. obs: 97517 / % possible obs: 99.97 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.6
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 7128 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
PHENIX1.9_1692phasing
xia2-3dadata reduction
xia2-3dadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NE4

4ne4


Resolution: 1.62→41.12 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.68
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 4874 5 %random
Rwork0.1585 ---
obs0.1599 97517 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 54 710 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064768
X-RAY DIFFRACTIONf_angle_d1.0856554
X-RAY DIFFRACTIONf_dihedral_angle_d12.6071778
X-RAY DIFFRACTIONf_chiral_restr0.04766
X-RAY DIFFRACTIONf_plane_restr0.005856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.26671750.22193051X-RAY DIFFRACTION100
1.6384-1.65770.23051530.21163018X-RAY DIFFRACTION100
1.6577-1.67790.25291570.20673052X-RAY DIFFRACTION100
1.6779-1.69920.24661410.20373052X-RAY DIFFRACTION100
1.6992-1.72150.23911650.19623075X-RAY DIFFRACTION100
1.7215-1.74510.20811550.18843035X-RAY DIFFRACTION100
1.7451-1.770.20371860.1863047X-RAY DIFFRACTION100
1.77-1.79650.2161540.18213065X-RAY DIFFRACTION100
1.7965-1.82450.22171640.17833028X-RAY DIFFRACTION100
1.8245-1.85440.20631710.1733069X-RAY DIFFRACTION100
1.8544-1.88640.19411500.16763067X-RAY DIFFRACTION100
1.8864-1.92070.20281460.16883059X-RAY DIFFRACTION100
1.9207-1.95770.20011610.16623065X-RAY DIFFRACTION100
1.9577-1.99760.19331700.16223046X-RAY DIFFRACTION100
1.9976-2.04110.19621630.16623071X-RAY DIFFRACTION100
2.0411-2.08850.1981280.16473093X-RAY DIFFRACTION100
2.0885-2.14080.18641560.15633080X-RAY DIFFRACTION100
2.1408-2.19860.17341640.15763081X-RAY DIFFRACTION100
2.1986-2.26330.1761740.15923076X-RAY DIFFRACTION100
2.2633-2.33640.17161780.16223030X-RAY DIFFRACTION100
2.3364-2.41990.20061650.16283114X-RAY DIFFRACTION100
2.4199-2.51680.19451780.16253062X-RAY DIFFRACTION100
2.5168-2.63130.19751730.16953072X-RAY DIFFRACTION100
2.6313-2.770.18141430.16773143X-RAY DIFFRACTION100
2.77-2.94350.19521860.15973071X-RAY DIFFRACTION100
2.9435-3.17070.19571560.16113154X-RAY DIFFRACTION100
3.1707-3.48960.19241560.14823149X-RAY DIFFRACTION100
3.4896-3.99420.14781770.12863151X-RAY DIFFRACTION100
3.9942-5.03080.13931700.12753199X-RAY DIFFRACTION100
5.0308-41.13940.19151590.16353368X-RAY DIFFRACTION99

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