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- PDB-5dz9: Streptococcus agalactiae AgI/II polypeptide BspA C-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 5dz9
TitleStreptococcus agalactiae AgI/II polypeptide BspA C-terminal domain (Mut)
ComponentsBspA
KeywordsCELL ADHESION / Adhesin / Streptococcus agalactiae
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
Adhesin BspA, variable domain / Adhesin BspA variable domain / 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. ...Adhesin BspA, variable domain / Adhesin BspA variable domain / 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
Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype III
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRego, S. / Till, M. / Race, P.R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae.
Authors: Rego, S. / Heal, T.J. / Pidwill, G.R. / Till, M. / Robson, A. / Lamont, R.J. / Sessions, R.B. / Jenkinson, H.F. / Race, P.R. / Nobbs, A.H.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BspA


Theoretical massNumber of molelcules
Total (without water)37,0951
Polymers37,0951
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.090, 48.240, 234.130
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 BspA


Mass: 37094.844 Da / Num. of mol.: 1 / Fragment: UNP residues 554-881 / Mutation: G744D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype III (strain NEM316) (bacteria)
Gene: gbs1143 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E589
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MMT buffer (1:2:2 L-Malic acid, MES, Tris-HCl pH 6.0) and 25% (w/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→58.53 Å / Num. obs: 35603 / % possible obs: 99.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.2
Reflection shellResolution: 1.89→1.94 Å / Rmerge(I) obs: 0.835 / Num. unique all: 2482

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Processing

Software
NameVersionClassification
PHASERphasing
Cootmodel building
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WOY

2woy


Resolution: 1.89→58.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.138 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24078 1778 5 %RANDOM
Rwork0.19468 ---
obs0.19693 33734 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.575 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--1.02 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.89→58.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 320 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192680
X-RAY DIFFRACTIONr_bond_other_d0.0010.022573
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9523634
X-RAY DIFFRACTIONr_angle_other_deg0.86935932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18825.868121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.394155
X-RAY DIFFRACTIONr_chiral_restr0.1290.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7812.0061343
X-RAY DIFFRACTIONr_mcbond_other1.7812.0051342
X-RAY DIFFRACTIONr_mcangle_it2.4162.9981679
X-RAY DIFFRACTIONr_mcangle_other2.4152.9981680
X-RAY DIFFRACTIONr_scbond_it2.7992.3131337
X-RAY DIFFRACTIONr_scbond_other2.7982.3131338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2813.3361952
X-RAY DIFFRACTIONr_long_range_B_refined6.20817.4723210
X-RAY DIFFRACTIONr_long_range_B_other6.01516.8833076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 113 -
Rwork0.361 2357 -
obs--95.81 %

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