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- PDB-6bgd: The crystal structure of the W145A variant of TpMglB-2 (Tp0684) w... -

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Basic information

Entry
Database: PDB / ID: 6bgd
TitleThe crystal structure of the W145A variant of TpMglB-2 (Tp0684) with bound ligand
ComponentsGlucose/galactose-binding lipoprotein
KeywordsSUGAR BINDING PROTEIN / glucose / syphilis
Function / homology
Function and homology information


: / plasma membrane
Similarity search - Function
MglB-2, periplasmic binding protein domain / Periplasmic binding protein domain / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose/galactose-binding lipoprotein
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsBrautigam, C.A. / Norgard, M.V. / Deka, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI056305 United States
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structures of MglB-2 (TP0684), a topologically variant d-glucose-binding protein from Treponema pallidum, reveal a ligand-induced conformational change.
Authors: Brautigam, C.A. / Deka, R.K. / Liu, W.Z. / Norgard, M.V.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 15, 2023Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose/galactose-binding lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,96612
Polymers40,3051
Non-polymers66111
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.834, 110.199, 89.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

21A-883-

HOH

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Components

#1: Protein Glucose/galactose-binding lipoprotein


Mass: 40304.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (strain Nichols) (bacteria)
Strain: Nichols / Gene: mglB, tpp38, TP_0684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08255
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na citrate 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.47→37.9 Å / Num. obs: 60862 / % possible obs: 95.4 % / Redundancy: 4.4 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JX2

5jx2


Resolution: 1.47→37.9 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.84
RfactorNum. reflection% reflection
Rfree0.1439 3082 5.06 %
Rwork0.1139 --
obs0.1154 60850 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 41 393 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092991
X-RAY DIFFRACTIONf_angle_d1.2644049
X-RAY DIFFRACTIONf_dihedral_angle_d12.5561092
X-RAY DIFFRACTIONf_chiral_restr0.078442
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4743-1.49730.20381390.1352407X-RAY DIFFRACTION90
1.4973-1.52190.21411330.11782558X-RAY DIFFRACTION94
1.5219-1.54810.16211390.11562590X-RAY DIFFRACTION96
1.5481-1.57630.14911360.10912615X-RAY DIFFRACTION96
1.5763-1.60660.15331240.10332595X-RAY DIFFRACTION96
1.6066-1.63940.14761220.10282648X-RAY DIFFRACTION97
1.6394-1.6750.16051570.09772572X-RAY DIFFRACTION95
1.675-1.7140.14151470.09532541X-RAY DIFFRACTION94
1.714-1.75690.14531390.09262610X-RAY DIFFRACTION97
1.7569-1.80440.15041450.09262660X-RAY DIFFRACTION98
1.8044-1.85750.14381230.09222655X-RAY DIFFRACTION97
1.8575-1.91740.14671560.08862627X-RAY DIFFRACTION97
1.9174-1.98590.13661400.09622609X-RAY DIFFRACTION96
1.9859-2.06540.13591160.09962597X-RAY DIFFRACTION95
2.0654-2.15940.15111130.10812694X-RAY DIFFRACTION98
2.1594-2.27330.13991630.10412637X-RAY DIFFRACTION98
2.2733-2.41570.14451470.10342661X-RAY DIFFRACTION97
2.4157-2.60210.13121580.11342567X-RAY DIFFRACTION94
2.6021-2.86390.14451680.12212696X-RAY DIFFRACTION99
2.8639-3.27810.12581500.12492718X-RAY DIFFRACTION99
3.2781-4.12930.15321300.12282704X-RAY DIFFRACTION96
4.1293-37.92950.13491370.14362807X-RAY DIFFRACTION96

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