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- PDB-2woy: Crystal structure of the C-terminal domain of Streptococcus gordo... -

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Basic information

Entry
Database: PDB / ID: 2woy
TitleCrystal structure of the C-terminal domain of Streptococcus gordonii surface protein SspB
ComponentsAGGLUTININ RECEPTOR
KeywordsCELL ADHESION / CELL WALL / ANTIGEN I/II / PEPTIDOGLYCAN-ANCHOR
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 / Immunoglobulin-like - #740 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS GORDONII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsForsgren, N. / Persson, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Two Intramolecular Isopeptide Bonds are Identified in the Crystal Structure of the Streptococcus Gordonii Sspb C-Terminal Domain.
Authors: Forsgren, N. / Lamont, R.J. / Persson, K.
History
DepositionJul 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 5, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1875
Polymers40,0261
Non-polymers1604
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.745, 50.290, 94.370
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AGGLUTININ RECEPTOR / SSPB-5


Mass: 40026.203 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1083-1413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS GORDONII (bacteria) / Strain: M5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16952
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M CACL2, 0.1 M HEPES PH 7.5, 20 % (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 9, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.5→50.32 Å / Num. obs: 55706 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 11.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→46.788 Å / SU ML: 0.19 / σ(F): 0.03 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 2740 5.1 %
Rwork0.1801 --
obs0.1815 53801 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.731 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 16.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.9897 Å20 Å2-4.3576 Å2
2---1.2665 Å2-0 Å2
3---0.3278 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 4 372 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112683
X-RAY DIFFRACTIONf_angle_d1.3323647
X-RAY DIFFRACTIONf_dihedral_angle_d16.303972
X-RAY DIFFRACTIONf_chiral_restr0.096416
X-RAY DIFFRACTIONf_plane_restr0.006476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52590.2726890.23311967X-RAY DIFFRACTION73
1.5259-1.55360.23631050.20032134X-RAY DIFFRACTION82
1.5536-1.58350.23411300.18422448X-RAY DIFFRACTION91
1.5835-1.61580.21941450.18682405X-RAY DIFFRACTION92
1.6158-1.6510.2561330.1812532X-RAY DIFFRACTION94
1.651-1.68940.22721280.17672497X-RAY DIFFRACTION96
1.6894-1.73160.21431350.172566X-RAY DIFFRACTION95
1.7316-1.77850.21771460.16682545X-RAY DIFFRACTION96
1.7785-1.83080.2011210.16562595X-RAY DIFFRACTION97
1.8308-1.88990.22361360.17262670X-RAY DIFFRACTION98
1.8899-1.95740.19151500.16692577X-RAY DIFFRACTION99
1.9574-2.03580.19841420.16772639X-RAY DIFFRACTION99
2.0358-2.12850.21061580.16612636X-RAY DIFFRACTION99
2.1285-2.24070.17791430.16142687X-RAY DIFFRACTION100
2.2407-2.3810.18971370.18242674X-RAY DIFFRACTION100
2.381-2.56490.22651400.18122667X-RAY DIFFRACTION100
2.5649-2.8230.18941550.17962670X-RAY DIFFRACTION100
2.823-3.23140.21051630.17922675X-RAY DIFFRACTION100
3.2314-4.07080.18271310.16392717X-RAY DIFFRACTION100
4.0708-46.81070.17031530.16022760X-RAY DIFFRACTION99
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)
10.2121-0.02170.02450.983-0.29990.20430.0545-0.0625-0.00920.228-0.0358-0.0786-0.0640.0108-0.00020.1197-0.0272-0.02420.12270.00930.0742-4.578321.346640.902
20.19430.03950.04670.2211-0.19640.332-0.00060.00660.00180.0160.0057-0.0190.00190.026-0.00710.04750.00620.00690.04390.00080.0565-28.448319.23076.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESID 1081:1253
2X-RAY DIFFRACTION2RESID 1254:1413

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