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- PDB-5dz8: Streptococcus agalactiae AgI/II polypeptide BspA variable (V) domain -

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Basic information

Entry
Database: PDB / ID: 5dz8
TitleStreptococcus agalactiae AgI/II polypeptide BspA variable (V) domain
ComponentsBspA (BspA_V)
KeywordsCELL ADHESION / Adhesin
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 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype III
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 (BspA_V)
B: BspA (BspA_V)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9335
Polymers37,7052
Non-polymers2273
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-11 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.140, 34.420, 92.600
Angle α, β, γ (deg.)90.00, 127.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BspA (BspA_V)


Mass: 18852.699 Da / Num. of mol.: 2 / Fragment: Variable (V) domain, UNP residues 285-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype III (strain NEM316) (bacteria)
Strain: NEM316 / Gene: gbs1143 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E589
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer System 1 at pH 6.5 (MES, imidazole), 0.1 M amino acids and 37.5% MPD_P1K_P3350 (Morpheus screen, Molecular Dimensions Ltd)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97935 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.41→73.65 Å / Num. obs: 14728 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.9
Reflection shellResolution: 2.41→2.54 Å / Rmerge(I) obs: 0.14 / Num. unique all: 2054

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.41→73.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.845 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23229 746 5.1 %RANDOM
Rwork0.17664 ---
obs0.17959 13981 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.402 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20.33 Å2
2--1.79 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.41→73.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 15 64 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192551
X-RAY DIFFRACTIONr_bond_other_d0.0020.022358
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9233448
X-RAY DIFFRACTIONr_angle_other_deg0.99335393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4895316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57325.366123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33715384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.545154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
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_it4.1294.6121286
X-RAY DIFFRACTIONr_mcbond_other4.1144.6091284
X-RAY DIFFRACTIONr_mcangle_it6.1546.8761594
X-RAY DIFFRACTIONr_mcangle_other6.1586.8771595
X-RAY DIFFRACTIONr_scbond_it5.0734.961265
X-RAY DIFFRACTIONr_scbond_other5.0654.961265
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5587.2561855
X-RAY DIFFRACTIONr_long_range_B_refined9.94436.0382590
X-RAY DIFFRACTIONr_long_range_B_other9.94436.0482591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 45 -
Rwork0.205 982 -
obs--93.96 %

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