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- PDB-5k2x: Crystal structure of M. tuberculosis UspC (tetragonal crystal form) -

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Basic information

Entry
Database: PDB / ID: 5k2x
TitleCrystal structure of M. tuberculosis UspC (tetragonal crystal form)
ComponentsSugar ABC transporter permease
KeywordsTRANSPORT PROTEIN / Mycobacterium tuberculosis / ABC transporter / solute binding protein
Function / homologyBacterial 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 / IODIDE ION / Sugar ABC transporter permease / Probable periplasmic sugar-binding lipoprotein UspC
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 1.2Jun 19, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,18417
Polymers45,2271
Non-polymers1,95716
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.850, 87.850, 52.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Sugar ABC transporter permease


Mass: 45227.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminally truncated sequence of M. tuberculosis UspC (Rv2318).
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: uspC, ERS007688_00434 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0T5Y5I3, UniProt: P71894*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M of 1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 1 M of imidazole, MES; 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.5→45.31 Å / Num. obs: 64354 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 3.2 / % possible all: 99

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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: 1.5→45.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.353 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 3218 5 %RANDOM
Rwork0.1623 ---
obs0.1636 61120 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.63 Å2 / Biso mean: 14.403 Å2 / Biso min: 4.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.5→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 26 463 3599
Biso mean--24.29 26.95 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193224
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9284406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9623.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.79415429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0681526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212576
X-RAY DIFFRACTIONr_mcbond_it0.6160.7211670
X-RAY DIFFRACTIONr_mcangle_it1.0771.0752091
X-RAY DIFFRACTIONr_scbond_it0.9260.8031554
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 237 -
Rwork0.203 4498 -
all-4735 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 30.418 Å / Origin y: 13.507 Å / Origin z: 1.891 Å
111213212223313233
T0.0162 Å20.0039 Å20.0114 Å2-0.0279 Å2-0.0037 Å2--0.0223 Å2
L0.3647 °2-0.0325 °20.3571 °2-0.3835 °20.0061 °2--0.7268 °2
S0.0168 Å °-0.0147 Å °-0.0044 Å °-0.0277 Å °-0.0234 Å °0.0384 Å °-0.0114 Å °-0.0412 Å °0.0066 Å °

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