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- PDB-5k2y: Crystal structure of M. tuberculosis UspC (monoclinic crystal form) -

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Basic information

Entry
Database: PDB / ID: 5k2y
TitleCrystal structure of M. tuberculosis UspC (monoclinic crystal form)
ComponentsProbable periplasmic sugar-binding lipoprotein UspC
KeywordsTRANSPORT PROTEIN / Mycobacterium tuberculosis / ABC transporter / solute binding protein
Function / homology: / cell envelope / 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 / Probable periplasmic sugar-binding lipoprotein UspC
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsFutterer, K. / Fullam, E. / Besra, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust / Royal society104193/Z/14/Z United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Structural and functional analysis of the solute-binding protein UspC from Mycobacterium tuberculosis that is specific for amino sugars.
Authors: Fullam, E. / Prokes, I. / Futterer, K. / Besra, G.S.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable periplasmic sugar-binding lipoprotein UspC
B: Probable periplasmic sugar-binding lipoprotein UspC


Theoretical massNumber of molelcules
Total (without water)89,4592
Polymers89,4592
Non-polymers00
Water93752
1
A: Probable periplasmic sugar-binding lipoprotein UspC


Theoretical massNumber of molelcules
Total (without water)44,7301
Polymers44,7301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable periplasmic sugar-binding lipoprotein UspC


Theoretical massNumber of molelcules
Total (without water)44,7301
Polymers44,7301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.990, 52.350, 87.890
Angle α, β, γ (deg.)90.000, 90.880, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 39 - 438 / Label seq-ID: 1 - 400

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable periplasmic sugar-binding lipoprotein UspC


Mass: 44729.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminally truncated UspC from Mycobacterium tuberculosis with C-terminal hexa-histidine tag from pET23b plasmid
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: uspC, Rv2318 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71894
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Precipitant mix: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 Halogen mix: 0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide Buffer: 1.0 M Imidazole; MES monohydrate (acid)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.41→87.9 Å / Num. obs: 30838 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 14.3
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 6 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.3 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→87.88 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.888 / SU B: 22.395 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.288
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 1551 5 %RANDOM
Rwork0.2025 ---
obs0.2054 29276 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 34.667 Å2 / Biso min: 7.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.48 Å2
2---0.01 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.41→87.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 0 52 5930
Biso mean---24.54 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196036
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9258275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69423.684266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.551534
X-RAY DIFFRACTIONr_chiral_restr0.1230.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214833
X-RAY DIFFRACTIONr_mcbond_it1.0312.1273198
X-RAY DIFFRACTIONr_mcangle_it1.8183.1873994
X-RAY DIFFRACTIONr_scbond_it0.9842.1112838
Refine LS restraints NCS

Ens-ID: 1 / Number: 994 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 106 -
Rwork0.289 2049 -
all-2155 -
obs--94.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5295-0.42340.11310.8127-0.01830.24630.0333-0.0319-0.0002-0.01380.0176-0.03520.01320.0326-0.05090.0779-0.0274-0.01330.09430.00880.113413.310.37913.801
20.20450.45310.50251.21670.89281.6997-0.05760.116-0.0801-0.11890.2303-0.0897-0.14370.3015-0.17260.0294-0.01820.00720.2297-0.05510.141955.72913.26729.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 438
2X-RAY DIFFRACTION2B39 - 438

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