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- PDB-2x9w: STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE -

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Basic information

Entry
Database: PDB / ID: 2x9w
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 / 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 / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain ...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 / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / 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 / SAD / Resolution: 1.92 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 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Jun 5, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4864
Polymers48,2101
Non-polymers2763
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.360, 74.063, 104.461
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 CELL WALL SURFACE ANCHOR FAMILY PROTEIN / RRGB


Mass: 48210.090 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.96 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 0.05 POTASSIUM DIHYDROGEN PHOSPHATE, 20% PEG-8000, PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→44.9 Å / Num. obs: 40524 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 22.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 0.95 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.92→44.977 Å / SU ML: 0.25 / σ(F): 0.14 / Phase error: 20.85 / Stereochemistry target values: ML
Details: THIS MODEL WAS REFINED WITH THE ANOMALOUS DATA (F+ AND F-).
RfactorNum. reflection% reflection
Rfree0.2276 3579 5.1 %
Rwork0.1738 --
obs0.1764 40524 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.659 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 30.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.5949 Å20 Å2-0 Å2
2--2.9559 Å20 Å2
3----2.8033 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 18 290 3679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113464
X-RAY DIFFRACTIONf_angle_d1.2944707
X-RAY DIFFRACTIONf_dihedral_angle_d16.8661253
X-RAY DIFFRACTIONf_chiral_restr0.084546
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9182-1.94340.3034780.32121747X-RAY DIFFRACTION62
1.9434-1.970.29061040.27372198X-RAY DIFFRACTION77
1.97-1.99820.26221260.25052223X-RAY DIFFRACTION79
1.9982-2.0280.27551320.22912313X-RAY DIFFRACTION83
2.028-2.05970.25521130.18312348X-RAY DIFFRACTION82
2.0597-2.09350.22231160.19922485X-RAY DIFFRACTION88
2.0935-2.12960.20331530.17812598X-RAY DIFFRACTION91
2.1296-2.16830.21191620.17622562X-RAY DIFFRACTION92
2.1683-2.210.28421530.19422550X-RAY DIFFRACTION92
2.21-2.25510.2781390.22632466X-RAY DIFFRACTION87
2.2551-2.30410.26891310.18772375X-RAY DIFFRACTION85
2.3041-2.35770.21871360.16642668X-RAY DIFFRACTION95
2.3577-2.41670.23951450.17092695X-RAY DIFFRACTION95
2.4167-2.4820.25221400.1672652X-RAY DIFFRACTION94
2.482-2.5550.20131750.16332646X-RAY DIFFRACTION95
2.555-2.63750.21541430.16282741X-RAY DIFFRACTION96
2.6375-2.73180.2721630.16422687X-RAY DIFFRACTION96
2.7318-2.84110.22131350.16442767X-RAY DIFFRACTION97
2.8411-2.97040.2441540.16052721X-RAY DIFFRACTION97
2.9704-3.1270.21641420.15962766X-RAY DIFFRACTION98
3.127-3.32280.18111510.15052767X-RAY DIFFRACTION99
3.3228-3.57930.18591420.14372806X-RAY DIFFRACTION98
3.5793-3.93930.21681440.15532784X-RAY DIFFRACTION99
3.9393-4.50890.22351170.14742832X-RAY DIFFRACTION99
4.5089-5.67890.19471360.16582829X-RAY DIFFRACTION100
5.6789-44.98910.21581490.19362807X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8428-0.21310.5720.5207-0.54841.1595-0.05450.01880.00860.0326-0.00420.0445-0.12720.04780.04760.17360.0064-0.00770.14050.010.159358.561147.588533.9546
21.1895-0.25170.00252.6981.12520.1488-0.1788-0.40970.15630.29530.12480.1324-0.0368-0.04310.06090.26790.0708-0.00930.2656-0.0340.179255.352856.394151.7073
31.2365-0.2923-0.03761.2035-0.30940.8179-0.0188-0.08340.00790.0611-0.0722-0.09770.01260.1810.08780.10780.0087-0.01110.14890.02850.126870.342617.356657.8791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 186:326
2X-RAY DIFFRACTION2CHAIN A AND RESID 327:445
3X-RAY DIFFRACTION3CHAIN A AND RESID 446:627

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