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- PDB-2wza: Two intramolecular isopeptide bonds are identified in the crystal... -

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Basic information

Entry
Database: PDB / ID: 2wza
TitleTwo intramolecular isopeptide bonds are identified in the crystal structure of the Streptococcus gordonii SspB C-terminal domain
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. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / 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 I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Antigen I/II, N-terminal / Adhesin P1 N-terminal domain / 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 / Cell surface antigen C-terminus / Cell surface antigen I/II C2 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 / MOLECULAR REPLACEMENT / Resolution: 2.082 Å
AuthorsForsgren, N. / Lamont, R.J. / 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
DepositionNov 26, 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 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jun 5, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8664
Polymers41,7461
Non-polymers1203
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.750, 80.150, 87.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGGLUTININ RECEPTOR / SSP-5


Mass: 41745.961 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1061-1413
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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M CACL2, 0.1 M HEPES, PH 7.5, 20% (W/V) PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→42.56 Å / Num. obs: 21137 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.09 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.77
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 6.86 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOY

2woy


Resolution: 2.082→42.578 Å / SU ML: 0.29 / σ(F): 0.1 / Phase error: 24.26 / Stereochemistry target values: ML
Details: THE LINKER RESIDUES AND RESIDUES 1061-1075 ARE DISORDERED AND NOT INCLUDED IN THE MODEL ONE ISOPEPTIDE BOND IS FORMED BETWEEN ASN1393 AND LYS1259 AND ONE ISOPEPTIDE BOND BETWEEN ASN1232 AND LYS1082
RfactorNum. reflection% reflection
Rfree0.255 1073 5.2 %
Rwork0.1923 --
obs0.1956 20786 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.965 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 25.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.5025 Å2-0 Å20 Å2
2---7.4428 Å2-0 Å2
3---5.6657 Å2
Refinement stepCycle: LAST / Resolution: 2.082→42.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 3 138 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122711
X-RAY DIFFRACTIONf_angle_d1.4083677
X-RAY DIFFRACTIONf_dihedral_angle_d18.463977
X-RAY DIFFRACTIONf_chiral_restr0.098417
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.082-2.17680.29761390.21412405X-RAY DIFFRACTION97
2.1768-2.29160.30621250.20442363X-RAY DIFFRACTION96
2.2916-2.43510.24591320.2062422X-RAY DIFFRACTION98
2.4351-2.62310.31111200.19472418X-RAY DIFFRACTION98
2.6231-2.8870.2471430.19992452X-RAY DIFFRACTION98
2.887-3.30470.24511360.1882487X-RAY DIFFRACTION99
3.3047-4.1630.22321370.17322533X-RAY DIFFRACTION100
4.163-42.58730.24191410.1872633X-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)
10.170.2542-0.12050.3551-0.06510.41810.0032-0.02230.0827-0.0082-0.05940.2022-0.0042-0.0778-00.08650.0021-0.02330.0892-0.04730.13379.194331.500213.6252
20.54590.24470.39550.4743-0.00240.608-0.00930.02930.0156-0.00310.01450.00480.04510.02530.02760.02120.00180.01120.0367-0.00790.02187.24-8.7782-0.361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESID 1076:1253
2X-RAY DIFFRACTION2RESID 1254:1413

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