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- PDB-3rpk: Structure of the Full-Length Major Pilin RrgB from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 3rpk
TitleStructure of the Full-Length Major Pilin RrgB from Streptococcus pneumoniae
ComponentsBackbone pilus subunit
KeywordsCELL ADHESION / Isopeptide bond / Ig-like fold / Cell wall / Peptidoglycan-anchor / STRUCTURAL PROTEIN
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / : ...Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / : / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell wall surface anchor family protein / Backbone pilus subunit
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPaterson, N.G. / Baker, E.N.
CitationJournal: Plos One / Year: 2011
Title: Structure of the Full-Length Major Pilin from Streptococcus pneumoniae: Implications for Isopeptide Bond Formation in Gram-Positive Bacterial Pili
Authors: Paterson, N.G. / Baker, E.N.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Nov 1, 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 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Backbone pilus subunit
B: Backbone pilus subunit


Theoretical massNumber of molelcules
Total (without water)130,2672
Polymers130,2672
Non-polymers00
Water0
1
A: Backbone pilus subunit


Theoretical massNumber of molelcules
Total (without water)65,1331
Polymers65,1331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Backbone pilus subunit


Theoretical massNumber of molelcules
Total (without water)65,1331
Polymers65,1331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.37, 107.93, 142.45
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 Backbone pilus subunit


Mass: 65133.422 Da / Num. of mol.: 2 / Fragment: UNP residues 29-628, domains D1-D4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: rrgB / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / References: UniProt: A7KT39, UniProt: A0A0H2UNM7*PLUS

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.9M ammonium sulfate, 0.1M Tris-HCl, 100mM ammonium iodide, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2009
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 30964 / Num. obs: 30964 / % possible obs: 95.5 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 46.78 Å2 / Rsym value: 0.2 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4554 / Rsym value: 0.75 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2X9W

2x9w


Resolution: 2.8→19.47 Å / Cor.coef. Fo:Fc: 0.8849 / Cor.coef. Fo:Fc free: 0.8162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 1570 5.09 %RANDOM
Rwork0.2174 ---
all0.2206 30964 --
obs0.2206 30817 --
Displacement parametersBiso mean: 29.02 Å2
Baniso -1Baniso -2Baniso -3
1--15.9006 Å20 Å20 Å2
2--6.0933 Å20 Å2
3---9.8073 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8964 0 0 0 8964
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3152SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes292HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1302HARMONIC5
X-RAY DIFFRACTIONt_it9140HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10129SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9140HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12450HARMONIC21.32
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion22.13
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3289 172 5.62 %
Rwork0.2321 2890 -
all0.2376 3062 -
obs-3062 -

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