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- PDB-3tw0: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B St... -

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Basic information

Entry
Database: PDB / ID: 3tw0
TitleStructural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / vWFA fold / Ancillary pilin / Gram-positive bacterial cell surface
Function / homology
Function and homology information


extracellular region / metal ion binding / membrane
Similarity search - Function
Alpha-Beta Plaits - #1830 / : / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain ...Alpha-Beta Plaits - #1830 / : / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Alpha-Beta Plaits / Immunoglobulin-like fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Cell wall surface anchor family protein, putative
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,89012
Polymers166,5574
Non-polymers3338
Water13,673759
1
A: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7223
Polymers41,6391
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7223
Polymers41,6391
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7223
Polymers41,6391
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7223
Polymers41,6391
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.071, 77.260, 96.402
Angle α, β, γ (deg.)74.12, 87.25, 89.99
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 41639.133 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Mutation: T564C, K571C
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN3 DOMAIN (UNP RESIDUES 212-581) REMAINS AFTER DEGRADATION OF ORIGINAL PROTEIN CONSTRUCT (UNP ...N3 DOMAIN (UNP RESIDUES 212-581) REMAINS AFTER DEGRADATION OF ORIGINAL PROTEIN CONSTRUCT (UNP RESIDUES 212-854) DURING CRYSTALLIZATION.

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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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3000, 0.1 M HEPES, 0.2 M NaCl, 10 mM Spermine-4HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.304 Å / Num. obs: 88454 / % possible obs: 89 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.2 / % possible all: 80.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TVY

3tvy


Resolution: 2→46.304 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.843 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23068 4418 5 %RANDOM
Rwork0.19826 ---
obs0.19987 84024 88.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.05 Å20.16 Å2
2--0.32 Å20.07 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→46.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 20 759 12159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211631
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9415784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59751435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99625.481582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.092151949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2571544
X-RAY DIFFRACTIONr_chiral_restr0.0980.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218956
X-RAY DIFFRACTIONr_mcbond_it0.7661.57167
X-RAY DIFFRACTIONr_mcangle_it1.374211605
X-RAY DIFFRACTIONr_scbond_it2.11934464
X-RAY DIFFRACTIONr_scangle_it3.3834.54179
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 259 -
Rwork0.281 5307 -
obs--75.92 %

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