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- PDB-7l0o: Streptococcus gordonii C123 Domain(s)-Structural and Functional A... -

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Basic information

Entry
Database: PDB / ID: 7l0o
TitleStreptococcus gordonii C123 Domain(s)-Structural and Functional Analysis
ComponentsAgglutinin receptor
KeywordsCELL ADHESION / Streptococcus gordonii / SspB / C-terminal Domain / Agglutinin receptor
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal ...Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchormann, N. / Deivanayagam, C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and functional analysis of the C-terminal region of Streptococcus gordonii SspB.
Authors: Schormann, N. / Purushotham, S. / Mieher, J.L. / Patel, M. / Wu, H. / Deivanayagam, C.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Agglutinin receptor
B: Agglutinin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7226
Polymers112,5622
Non-polymers1604
Water73941
1
A: Agglutinin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3613
Polymers56,2811
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agglutinin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3613
Polymers56,2811
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.049, 109.140, 204.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 916 through 958 or resid 960...
21(chain B and (resid 916 through 1263 or resid 1278 through 1407 or resid 1502 through 1503))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 916 through 958 or resid 960...A916 - 958
121(chain A and (resid 916 through 958 or resid 960...A960 - 1018
131(chain A and (resid 916 through 958 or resid 960...A1021 - 1407
141(chain A and (resid 916 through 958 or resid 960...A1502 - 1503
211(chain B and (resid 916 through 1263 or resid 1278 through 1407 or resid 1502 through 1503))B916 - 1263
221(chain B and (resid 916 through 1263 or resid 1278 through 1407 or resid 1502 through 1503))B1278 - 1407
231(chain B and (resid 916 through 1263 or resid 1278 through 1407 or resid 1502 through 1503))B1502 - 1503

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Components

#1: Protein Agglutinin receptor / SSP-5


Mass: 56281.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: ssp5, sspB / Plasmid: pET23-d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16952
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.9 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.5M NaCl, 0.1M citric acid, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.592 Å / Num. obs: 60235 / % possible obs: 97.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.065 / Rrim(I) all: 0.167 / Χ2: 0.96 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.102 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4493 / CC1/2: 0.669 / Rpim(I) all: 0.863 / Rrim(I) all: 2.276 / Χ2: 0.94 / % possible all: 99

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA0.7.3data scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QE5, 2WOY

3qe5

2woy


Resolution: 2.7→48.592 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 2844 4.74 %
Rwork0.2184 57139 -
obs0.2201 59983 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.54 Å2 / Biso mean: 89.7616 Å2 / Biso min: 45.35 Å2
Refinement stepCycle: final / Resolution: 2.7→48.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7466 0 4 41 7511
Biso mean--125.81 64.84 -
Num. residues----955
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2830X-RAY DIFFRACTION9.933TORSIONAL
12B2830X-RAY DIFFRACTION9.933TORSIONAL
LS refinement shellResolution: 2.7→2.7466 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4132 140 -
Rwork0.3716 2882 -
obs--98 %
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)
11.4212-0.77360.00253.9748-0.73991.892-0.08430.18620.5677-0.30810.0234-0.0273-0.41720.0561-0.04230.8307-0.0581-0.25530.14970.07561.1287-31.433233.07616.2426
21.5113-1.43371.12713.772-3.02632.43530.08610.2618-0.0661-0.0236-0.0479-0.21050.61090.37060.07930.9790.1127-0.22290.2338-0.00750.8053-18.3695-3.327620.7805
30.02770.1956-0.09351.0751-0.56080.28820.0464-0.1723-0.2640.34880.37050.64170.1837-0.2816-0.22731.45420.0547-0.20450.17940.17121.0849-17.3173-29.577845.372
41.46540.09940.63496.6222.21732.9149-0.17310.3085-0.4947-0.82130.0081-0.07580.0549-0.04690.14590.8385-0.1550.20030.299-0.11070.9473-3.5028-84.5394-0.7174
50.61570.4605-0.15013.57382.5232.2161-0.34020.12160.112-0.3464-0.04760.1038-0.5287-0.33170.28721.13750.0916-0.26410.1736-0.05860.8281-5.0998-46.485118.9948
60.54840.1768-0.06322.60490.84360.86250.1469-0.00490.0974-0.13830.2136-0.615-0.20110.257-0.40021.3719-0.0668-0.28930.1687-0.11561.08696.839-15.057741.8257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 915 through 1078 )A915 - 1078
2X-RAY DIFFRACTION2chain 'A' and (resid 1079 through 1227 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1228 through 1407 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 916 through 1072 )B916 - 1072
5X-RAY DIFFRACTION5chain 'B' and (resid 1073 through 1260 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1261 through 1407 )B0

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