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- PDB-3phs: Crystal Structure of GBS52, the minor pilin in gram-positive path... -

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Basic information

Entry
Database: PDB / ID: 3phs
TitleCrystal Structure of GBS52, the minor pilin in gram-positive pathogen Streptococcus agalactiae
ComponentsCell wall surface anchor family protein
KeywordsStructural protein / CELL AHDESION / Ig-like fold / IgG-rev fold / GBS52 / Streptococcus agalactiae / gram-positive pilins / adhesions / CELL ADHESION / cell wall anchoring / adhesion / pilus subunit / isopeptide bond / Gram-positive bacterial cell wall
Function / homology
Function and homology information


extracellular region / membrane
Similarity search - Function
Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell wall surface anchor family protein
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsNarayana, S.V.L. / Krishnan, V.
Citation
Journal: Structure / Year: 2007
Title: An IgG-like domain in the minor pilin GBS52 of Streptococcus agalactiae mediates lung epithelial cell adhesion.
Authors: Krishnan, V. / Gaspar, A.H. / Ye, N. / Mandlik, A. / Ton-That, H. / Narayana, S.V.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2010ID: 2PZ4
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)27,6921
Polymers27,6921
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.481, 52.222, 61.006
Angle α, β, γ (deg.)90.00, 101.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell wall surface anchor family protein


Mass: 27692.242 Da / Num. of mol.: 1 / Fragment: GBS052 (unp residues 31-267)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: 2603V/R / Gene: GBS052, SAG0646 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLue / References: UniProt: Q8E0S8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG1500, 0.1M HEPES buffer, 0.2M Ammonium Citrate, 0.01M CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→26.81 Å / Num. all: 23655 / Num. obs: 23655 / % possible obs: 99.4 % / Redundancy: 3.01 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.33 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→26.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.643 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23042 1216 5.1 %RANDOM
Rwork0.19914 ---
obs0.20079 22438 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.81 Å2
2--0.41 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 0 215 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221901
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9692579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90525.66383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.349157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211411
X-RAY DIFFRACTIONr_mcbond_it0.6961.51186
X-RAY DIFFRACTIONr_mcangle_it1.32421929
X-RAY DIFFRACTIONr_scbond_it2.2593715
X-RAY DIFFRACTIONr_scangle_it3.8474.5649
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 79 -
Rwork0.369 1590 -
obs--96.47 %

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