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- PDB-5uqz: Structural Analysis of the Glucan Binding Protein C of Streptococ... -

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Basic information

Entry
Database: PDB / ID: 5uqz
TitleStructural Analysis of the Glucan Binding Protein C of Streptococcus mutans Provides Evidence that it Mediates both Sucrose-Independent and -Dependent Adherence
ComponentsGlucan-binding protein C, GbpC
KeywordsSUGAR BINDING PROTEIN / sugar binding / beta-supersandwich / glucan
Function / homologyGlucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / metal ion binding / Glucan-binding protein C, GbpC
Function and homology information
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.149 Å
AuthorsLarson, M.R. / Purushotham, S. / Mieher, J. / Wu, R. / Rajashankar, K.R. / Wu, H. / Deivanayagam, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE022350 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE017954 United States
CitationJournal: Infect. Immun. / Year: 2018
Title: Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence.
Authors: Mieher, J.L. / Larson, M.R. / Schormann, N. / Purushotham, S. / Wu, R. / Rajashankar, K.R. / Wu, H. / Deivanayagam, C.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucan-binding protein C, GbpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2932
Polymers39,2531
Non-polymers401
Water9,494527
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glucan-binding protein C, GbpC
hetero molecules

A: Glucan-binding protein C, GbpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5864
Polymers78,5062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3240 Å2
ΔGint-40 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.098, 48.596, 40.775
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

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Components

#1: Protein Glucan-binding protein C, GbpC


Mass: 39252.910 Da / Num. of mol.: 1 / Fragment: UNP residues 124-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Strain: ATCC 700610 / UA159 / Gene: gbpC, SMU_1396 / Plasmid: PET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DTF1
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.67 Å3/Da / Density % sol: 53.97 % / Mosaicity: 0.355 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2013
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 142968 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.28 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.121 / Net I/σ(I): 7.5 / Num. measured all: 518169
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.15-1.173.50.670211.006195.9
1.17-1.193.60.53270030.989196
1.19-1.213.50.48970081.012195.8
1.21-1.243.50.45171231.006196.9
1.24-1.273.40.40670761.011196.8
1.27-1.33.20.36869531.067195.1
1.3-1.333.50.32370041.058195.7
1.33-1.363.70.27470761.066196.7
1.36-1.43.60.2472041.076197.6
1.4-1.453.60.2171201.077197.5
1.45-1.53.60.16771691.118197.7
1.5-1.563.40.13771051.189196.8
1.56-1.633.60.11371521.202197
1.63-1.723.90.09772511.208199.3
1.72-1.833.90.07972911.224199
1.83-1.973.80.06472761.332198.9
1.97-2.163.60.05371291.305196.4
2.16-2.483.90.04772651.309198.4
2.48-3.123.90.04173881.15199.3
3.12-503.80.02973540.927197.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
SHELXEphasing
HKL-2000data reduction
HKLdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.149→40.53 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 13.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1463 10836 8.01 %
Rwork0.1238 124430 -
obs0.1256 135266 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.89 Å2 / Biso mean: 18.3548 Å2 / Biso min: 5.74 Å2
Refinement stepCycle: final / Resolution: 1.149→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 1 527 3297
Biso mean--9.73 32.72 -
Num. residues----354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1493-1.16240.2483330.21493506383978
1.1624-1.1760.22683130.19613759407283
1.176-1.19040.19963370.18613746408384
1.1904-1.20550.20833330.18573820415385
1.2055-1.22130.21053150.18283888420385
1.2213-1.2380.21663610.17313819418086
1.238-1.25570.18273210.16193901422286
1.2557-1.27450.18743280.15193876420486
1.2745-1.29440.18143270.15583900422786
1.2944-1.31560.18913270.14273955428287
1.3156-1.33830.15733380.13643954429290
1.3383-1.36260.1663490.13374123447291
1.3626-1.38890.16483630.12264156451992
1.3889-1.41720.15723640.12244200456493
1.4172-1.4480.13973470.11554161450893
1.448-1.48170.13573820.10584189457193
1.4817-1.51880.13113510.10484309466094
1.5188-1.55980.13223650.10064190455593
1.5598-1.60570.12833400.09624224456493
1.6057-1.65760.13853940.09874355474997
1.6576-1.71680.13124300.1034375480598
1.7168-1.78550.12923830.10434428481198
1.7855-1.86680.13983630.10624458482198
1.8668-1.96520.1333910.10374400479198
1.9652-2.08830.11533930.10494463485699
2.0883-2.24960.13893910.11394242463394
2.2496-2.47590.14773600.12044517487799
2.4759-2.83410.13774370.13254479491699
2.8341-3.57040.1434070.12194528493599
3.5704-40.55470.13883930.13014509490296

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