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- PDB-4mfi: Crystal structure of Mycobacterium tuberculosis UgpB -

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Basic information

Entry
Database: PDB / ID: 4mfi
TitleCrystal structure of Mycobacterium tuberculosis UgpB
ComponentsSn-glycerol-3-phosphate ABC transporter substrate-binding protein UspB
KeywordsSUGAR BINDING PROTEIN / alpha/beta domains / ABC transporter substrate-binding protein / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sn-glycerol-3-phosphate ABC transporter substrate-binding protein UspB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJiang, D. / Bartlam, M. / Rao, Z.
CitationJournal: Febs J. / Year: 2014
Title: Structural analysis of Mycobacterium tuberculosis ATP-binding cassette transporter subunit UgpB reveals specificity for glycerophosphocholine
Authors: Jiang, D. / Zhang, Q. / Zheng, Q. / Zhou, H. / Jin, J. / Zhou, W. / Bartlam, M. / Rao, Z.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sn-glycerol-3-phosphate ABC transporter substrate-binding protein UspB


Theoretical massNumber of molelcules
Total (without water)46,7721
Polymers46,7721
Non-polymers00
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.745, 72.200, 41.817
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-696-

HOH

21A-942-

HOH

31A-947-

HOH

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Components

#1: Protein Sn-glycerol-3-phosphate ABC transporter substrate-binding protein UspB


Mass: 46772.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: MRA_2856, ugpB / Production host: Escherichia coli (E. coli) / References: UniProt: A5U6I5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M sodium citrate, 0.2M sodium chloride, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 24, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 73135 / Num. obs: 73135 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→35.845 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 12.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1566 2000 2.73 %Random
Rwork0.1353 ---
obs0.1359 73132 99.49 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.043 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1263 Å20 Å2-1.1261 Å2
2---0.3324 Å20 Å2
3----0.7939 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 0 513 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063187
X-RAY DIFFRACTIONf_angle_d1.0454347
X-RAY DIFFRACTIONf_dihedral_angle_d11.2331118
X-RAY DIFFRACTIONf_chiral_restr0.077468
X-RAY DIFFRACTIONf_plane_restr0.006574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.53480.18251370.1346486697
1.5348-1.57630.18131430.12185073100
1.5763-1.62270.15271420.11095074100
1.6227-1.67510.16681430.11075091100
1.6751-1.73490.15361430.10885074100
1.7349-1.80440.13761430.1095080100
1.8044-1.88650.1321420.11095075100
1.8865-1.9860.14881450.12025148100
1.986-2.11040.15061420.13015041100
2.1104-2.27330.1551430.12925100100
2.2733-2.5020.16461440.13655119100
2.502-2.86390.17321440.15245120100
2.8639-3.60770.15771440.14815150100
3.6077-35.85550.15151450.1582512198

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