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- PDB-5cx8: Structure of RagB, a major immunodominant virulence factor of Por... -

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Basic information

Entry
Database: PDB / ID: 5cx8
TitleStructure of RagB, a major immunodominant virulence factor of Porphyromonas gingivalis.
ComponentsLipoprotein RagB
KeywordsMEMBRANE PROTEIN / Major immunodominant virulence factor
Function / homology
Function and homology information


SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
3-deoxy-beta-D-glucopyranose / ACETATE ION / 3-deoxy-5-O-phosphono-beta-D-ribofuranose / 6-O-phosphono-D-tagatose / Lipoprotein RagB
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGoulas, T. / Garcia-Ferrer, I. / Hutcherson, J.A. / Potempa, B.A. / Potempa, J. / Scott, D.A. / Gomis-Ruth, F.X.
Funding support United States, Spain, 8items
OrganizationGrant numberCountry
Grants DAVEUMO-2012/04/A/NZ1/00051 United States
Grants DAVEUMO-2012/05/B/NZ6/00581 United States
Grants DAVEUMO-2013/08/W/NZ1/00696 United States
European UnionFP7-PEOPLE-2011-ITN-290246 Spain
European UnionFP7-HEALTH-2012-306029-2 Spain
European UnionBFU2012-32862 Spain
Spanish Ministry for Education, Culture and SportJCI-2012-13573 Spain
Spanish Ministry for Education, Culture and SportAP2010-3799 Spain
CitationJournal: Mol Oral Microbiol / Year: 2016
Title: Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis.
Authors: Goulas, T. / Garcia-Ferrer, I. / Hutcherson, J.A. / Potempa, B.A. / Potempa, J. / Scott, D.A. / Xavier Gomis-Ruth, F.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein RagB
B: Lipoprotein RagB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,25110
Polymers109,2182
Non-polymers1,0338
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint0 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.640, 184.740, 144.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lipoprotein RagB


Mass: 54609.090 Da / Num. of mol.: 2 / Fragment: UNP residues 21-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: ragB, PG_0186 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F5H948

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-3DO / 3-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DGlcp[3H]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
3-deoxy-b-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-3-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-RP3 / 3-deoxy-5-O-phosphono-beta-D-ribofuranose


Type: D-saccharide, beta linking / Mass: 214.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O7P
IdentifierTypeProgram
b-D-3-deoxy-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 515 molecules

#3: Chemical ChemComp-TG6 / 6-O-phosphono-D-tagatose


Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM 2-(N-morpholino)ethanesulfonic acid 200mM calcium acetate, 20% [w/v] polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→48.3 Å / Num. obs: 60274 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 48.26 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
XDS2.10.2data reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTER2.10.2refinement
RefinementMethod to determine structure: SAD / Resolution: 2.4→35.14 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.9184 / SU R Cruickshank DPI: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 881 1.46 %RANDOM
Rwork0.1776 ---
obs0.178 60258 99.99 %-
Displacement parametersBiso mean: 56.01 Å2
Baniso -1Baniso -2Baniso -3
1-9.8211 Å20 Å20 Å2
2--8.2859 Å20 Å2
3----18.1069 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: 1 / Resolution: 2.4→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7528 0 66 509 8103
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0310549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3572SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1118HARMONIC5
X-RAY DIFFRACTIONt_it7773HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion991SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9178SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2541 66 1.48 %
Rwork0.2191 4381 -
all0.2196 4447 -
obs--99.99 %
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)
10.44590.0936-0.1820.6386-0.08690.378-0.04650.0233-0.0902-0.07470.0216-0.06880.0203-0.00280.0249-0.1922-0.0057-0.0111-0.0821-0.01140.056836.73122.478271.5917
21.1513-0.66070.31053.4109-0.1891.2536-0.1986-0.3752-0.13081.30190.2142-0.0346-0.1302-0.0235-0.01560.41040.0833-0.04010.09510.0394-0.086629.063837.754115.6
30.0515-0.26330.2800.801800.00010.01950.0005-0.04130.0015-0.01930.04620.0049-0.0016-0.09260.0967-0.17490.132-0.060.074634.565119.155552.2283
40.4131-0.06560.81240-0.24420.2124-0.00960.0255-0.0050.0038-0.00450.0209-0.00670.06380.0142-0.05170.0965-0.04790.1614-0.0467-0.093128.828325.294293.3358
50-0.0078-0.077500.04840-0.00040.0062-0.00530.01530.00180.00310.0088-0.0006-0.00140.05450.05570.0431-0.0578-0.10910.051219.254129.112590.1187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|30 - 501}
2X-RAY DIFFRACTION2{B|30 - 501}
3X-RAY DIFFRACTION3{L|3 - 3}
4X-RAY DIFFRACTION4{L|1 - 1}
5X-RAY DIFFRACTION5{L|2 - 2}

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