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

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Basic information

Entry
Database: PDB / ID: 6bgc
TitleThe crystal structure of the W145A variant of TpMglB-2 (Tp0684) with bound glucose
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
beta-D-glucopyranose / Glucose/galactose-binding lipoprotein
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.082 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 / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Glucose/galactose-binding lipoprotein
B: Glucose/galactose-binding lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8898
Polymers83,3252
Non-polymers5656
Water3,837213
1
A: Glucose/galactose-binding lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9454
Polymers41,6621
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucose/galactose-binding lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9454
Polymers41,6621
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.257, 61.592, 70.350
Angle α, β, γ (deg.)80.22, 77.58, 72.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucose/galactose-binding lipoprotein


Mass: 41662.316 Da / Num. of mol.: 2
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.0 200 mM NaCl 20% (w/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→39.73 Å / Num. obs: 36146 / % possible obs: 91.8 % / Redundancy: 2.5 % / Net I/σ(I): 9.8

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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: 2.082→39.728 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.03
RfactorNum. reflection% reflection
Rfree0.2199 1795 4.97 %
Rwork0.1803 --
obs0.1823 36128 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.082→39.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 34 213 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035655
X-RAY DIFFRACTIONf_angle_d0.6987660
X-RAY DIFFRACTIONf_dihedral_angle_d12.4352039
X-RAY DIFFRACTIONf_chiral_restr0.027860
X-RAY DIFFRACTIONf_plane_restr0.0031009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0816-2.13780.2381150.22522576X-RAY DIFFRACTION90
2.1378-2.20070.24441400.21412648X-RAY DIFFRACTION92
2.2007-2.27180.28771340.21472553X-RAY DIFFRACTION88
2.2718-2.35290.24691440.20962641X-RAY DIFFRACTION90
2.3529-2.44710.27771320.20732643X-RAY DIFFRACTION94
2.4471-2.55850.25851230.19452723X-RAY DIFFRACTION93
2.5585-2.69340.21221370.19742619X-RAY DIFFRACTION92
2.6934-2.86210.23281540.19762529X-RAY DIFFRACTION89
2.8621-3.0830.24271540.19652736X-RAY DIFFRACTION95
3.083-3.39310.23671560.18512683X-RAY DIFFRACTION94
3.3931-3.88370.21321350.16792630X-RAY DIFFRACTION91
3.8837-4.89160.16551370.13712709X-RAY DIFFRACTION94
4.8916-39.73530.18111340.15842643X-RAY DIFFRACTION92
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)
10.7242-0.5926-0.66211.4456-0.5641.7078-0.0219-0.08630.02940.329-0.0688-0.0987-0.01650.16490.07220.169-0.0286-0.06210.22540.00730.1621-12.349124.8838-85.1049
21.2786-0.2446-0.31921.63740.24271.8797-0.1347-0.2122-0.23070.2866-0.0448-0.18180.21020.38430.1670.27350.01990.00260.29340.02010.222-11.530913.2929-78.1916
31.2318-0.4143-0.07312.1927-0.66741.4487-0.24440.0472-0.33150.0447-0.00850.09040.65090.1520.24710.41810.03860.10550.2431-0.00350.2737-12.50015.6854-89.2067
41.34390.4989-0.68522.4997-0.51721.28930.10390.17880.1902-0.11320.05560.2966-0.1071-0.143-0.11870.1860.006-0.00980.24960.01630.1889-19.752934.8835-95.3677
50.327-0.32770.05231.5119-0.33450.99890.0750.15150.0148-0.4106-0.0520.16130.0727-0.1148-0.05240.26310.0237-0.0230.28450.0160.2437-18.011327.9995-100.595
61.038-0.0644-0.45192.5003-0.42721.36480.20270.08630.1063-0.4934-0.2928-0.65410.00710.28730.04010.2560.01180.07940.30010.08330.3224-2.519134.9068-101.1126
70.70660.08160.12921.55540.66311.0114-0.0548-0.0385-0.12180.2364-0.13260.340.3308-0.06340.17720.2488-0.02470.05460.1907-0.00730.225-23.131640.1839-54.4527
80.8435-0.2722-0.24092.0840.0271.11410.02430.06580.0086-0.0345-0.12550.1924-0.0438-0.11190.08670.13150.0066-0.00940.21-0.0120.1836-23.829966.3796-53.2009
90.3748-0.6311-0.09042.04641.02490.6928-0.0354-0.00760.01820.38630.0631-0.21610.25710.1137-0.00480.24590.0338-0.05070.2411-0.02070.2173-9.537946.1352-53.9026
100.7868-0.1851-0.26711.90090.75351.36420.01780.0577-0.0097-0.1644-0.10850.1420.1056-0.10640.07950.23010.00940.00360.2229-0.00420.1867-17.846537.5081-67.8883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 317 )
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 377 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 64 )
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 292 )
10X-RAY DIFFRACTION10chain 'B' and (resid 293 through 377 )

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