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- PDB-2x9y: STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE -

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Basic information

Entry
Database: PDB / ID: 2x9y
TitleSTRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsCELL ADHESION
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 / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Prealbumin-like fold domain / Prealbumin-like fold domain ...Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cell wall surface anchor family protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsSpraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. ...Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / Masignani, V. / Ferlenghi, I.
CitationJournal: Plos One / Year: 2010
Title: Supramolecular Organization of the Repetitive Backbone Unit of the Streptococcus Pneumoniae Pilus.
Authors: Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / ...Authors: Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / Masignani, V. / Ferlenghi, I.
History
DepositionMar 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)48,1631
Polymers48,1631
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.667, 157.745, 147.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN / RRGB


Mass: 48163.195 Da / Num. of mol.: 1 / Fragment: BACKBONE SUBUNIT PILI, RESIDUES 184-627 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE-BOND LINKS N318 AND K193, N428 AND K349, N623 AND K453
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: SPEEDET / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97SC2, UniProt: A0A0H2UNM7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 374 TO ALA

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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: 2.89 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 30% PEG-4000 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.54
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21514 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.7
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.34 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X9W

2x9w


Resolution: 2.33→42.084 Å / SU ML: 0.99 / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 1092 5.1 %
Rwork0.1999 --
obs0.2028 21265 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.2 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--13.9681 Å2-0 Å2-0 Å2
2---10.0668 Å20 Å2
3----28.742 Å2
Refinement stepCycle: LAST / Resolution: 2.33→42.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 0 256 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043335
X-RAY DIFFRACTIONf_angle_d0.7644551
X-RAY DIFFRACTIONf_dihedral_angle_d15.5681168
X-RAY DIFFRACTIONf_chiral_restr0.049537
X-RAY DIFFRACTIONf_plane_restr0.002599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.43610.28341050.23012189X-RAY DIFFRACTION83
2.4361-2.56450.3271350.23542343X-RAY DIFFRACTION90
2.5645-2.72510.32161530.22642482X-RAY DIFFRACTION96
2.7251-2.93550.27341350.22182516X-RAY DIFFRACTION97
2.9355-3.23080.25331320.20172571X-RAY DIFFRACTION98
3.2308-3.69810.26121340.17462620X-RAY DIFFRACTION98
3.6981-4.65820.19681500.15752652X-RAY DIFFRACTION99
4.6582-42.09120.20341480.17072800X-RAY DIFFRACTION100

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