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- PDB-3txa: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B St... -

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Basic information

Entry
Database: PDB / ID: 3txa
TitleStructural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / vWFA fold / IgG-like fold / Ancillary pilin / Gram-positive bacterial cell surface
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2110 / : / Tip pilin GBS104-like, Ig-like domain / Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Immunoglobulin-like - #2110 / : / Tip pilin GBS104-like, Ig-like domain / Prealbumin-like fold domain / Prealbumin-like fold domain / von Willebrand factor type A domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Cell wall surface anchor family protein, putative
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.619 Å
AuthorsKrishnan, V. / Narayana, S.V.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions.
Authors: Krishnan, V. / Dwivedi, P. / Kim, B.J. / Samal, A. / Macon, K. / Ma, X. / Mishra, A. / Doran, K.S. / Ton-That, H. / Narayana, S.V.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Aug 25, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17710
Polymers76,3591
Non-polymers8189
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.585, 124.585, 117.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cell wall surface anchor family protein / GBS104 / adhesive tip pilin


Mass: 76358.750 Da / Num. of mol.: 1 / Fragment: N2 and N3 domains (UNP residues 48-729)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: 2603 V/R / Gene: SAG0649 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8E0S5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG4000, 0.1 M Tris, pH 8.0, 0.2 M lithium sulfate, 10 mM cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.619→39.788 Å / Num. obs: 32251 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.096 / Net I/σ(I): 21.9
Reflection shellResolution: 2.619→2.67 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.67 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TVY

3tvy


Resolution: 2.619→39.788 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.023 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25552 1633 5.1 %RANDOM
Rwork0.20591 ---
obs0.20836 30583 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.557 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å21.16 Å20 Å2
2--2.32 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.619→39.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 9 79 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224702
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9516365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41925.764229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56915827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7661517
X-RAY DIFFRACTIONr_chiral_restr0.1030.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213573
X-RAY DIFFRACTIONr_mcbond_it0.891.52897
X-RAY DIFFRACTIONr_mcangle_it1.68424703
X-RAY DIFFRACTIONr_scbond_it2.31431805
X-RAY DIFFRACTIONr_scangle_it4.0294.51662
LS refinement shellResolution: 2.619→2.687 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 139 -
Rwork0.306 2199 -
obs--99.74 %

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