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- PDB-3klq: Crystal Structure of the Minor Pilin FctB from Streptococcus pyog... -

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Basic information

Entry
Database: PDB / ID: 3klq
TitleCrystal Structure of the Minor Pilin FctB from Streptococcus pyogenes 90/306S
ComponentsPutative pilus anchoring protein
KeywordsCELL ADHESION / CnaB fold / inverse IgG fold / polyproline-II-like helix
Function / homologyImmunoglobulin-like - #3050 / Streptococcal pilin isopeptide linker / Spy0128-like isopeptide containing domain / Streptococcal pilin isopeptide linker superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Putative pilus anchoring protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.9 Å
AuthorsLinke, C. / Young, P.G. / Bunker, R.D. / Caradoc-Davies, T.T. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the minor pilin FctB reveals determinants of Group A streptococcal pilus anchoring
Authors: Linke, C. / Young, P.G. / Kang, H.J. / Bunker, R.D. / Middleditch, M.J. / Caradoc-Davies, T.T. / Proft, T. / Baker, E.N.
History
DepositionNov 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: Putative pilus anchoring protein
B: Putative pilus anchoring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1174
Polymers30,9332
Non-polymers1842
Water4,161231
1
A: Putative pilus anchoring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6513
Polymers15,4661
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative pilus anchoring protein


Theoretical massNumber of molelcules
Total (without water)15,4661
Polymers15,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.192, 95.192, 100.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative pilus anchoring protein


Mass: 15466.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: 90/306S / Gene: fctB / Plasmid: pProEx Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL / References: UniProt: D2KPJ6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 4.25 Å3/Da / Density % sol: 71.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M Na-citrate, 0.1M Na-cadoylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→19.555 Å / Num. obs: 40679 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-27.60.5311.44491059340.531100
2-2.127.60.3282.34249455960.328100
2.12-2.277.60.2063.74021852960.206100
2.27-2.457.60.1495.23727648930.149100
2.45-2.697.60.1067.23447845260.106100
2.69-37.60.07110.23117541030.071100
3-3.477.50.049132734936250.049100
3.47-4.257.40.043142257330310.043100
4.25-6.017.40.03914.81776423970.039100
6.01-19.567.50.03913.6956612780.03997.1

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SCALAdata scaling
RefinementMethod to determine structure: SIR / Resolution: 1.9→19.554 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.03 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 2006 4.93 %
Rwork0.1585 --
obs0.1597 40653 99.98 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.364 Å2 / ksol: 0.437 e/Å3
Displacement parametersBiso max: 168.11 Å2 / Biso mean: 41.829 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.668 Å20 Å2-0 Å2
2--0.668 Å20 Å2
3----1.336 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 12 231 2273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064328
X-RAY DIFFRACTIONf_angle_d0.7747840
X-RAY DIFFRACTIONf_chiral_restr0.082373
X-RAY DIFFRACTIONf_plane_restr0.004658
X-RAY DIFFRACTIONf_dihedral_angle_d11.2251141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.9470.2261380.21627582896
1.947-20.1991490.18427482897
2-2.0590.2171320.1727492881
2.059-2.1250.1921530.16327302883
2.125-2.2010.1661350.15227832918
2.201-2.2890.1841570.15127252882
2.289-2.3930.181570.15427452902
2.393-2.5190.1871450.14927602905
2.519-2.6770.1751450.14927482893
2.677-2.8830.1891290.16327982927
2.883-3.1720.2061500.15627362886
3.172-3.6280.1841540.14427492903
3.628-4.5610.1641300.13927952925
4.561-19.5550.1481320.16628232955
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)
11.3368-0.4944-0.7968-0.05250.00783.20550.2212-0.02360.22080.0265-0.2062-0.1501-0.60740.096-0.07340.26820.00280.03820.12890.01020.21569.995565.74963.0201
2-0.3628-0.87960.61854.587-2.5041-1.31390.06140.02630.2054-0.1318-0.2410.4908-0.1322-0.01870.16540.76440.09840.01340.27340.0040.52712.385186.8409-6.6587
31.9205-0.88050.76771.0416-0.99692.61610.00260.0201-0.0936-0.09870.03290.00770.2098-0.0207-0.02560.1710.02530.02220.1368-0.00080.17089.558648.5142-7.0061
42.65160.4249-2.69512.1858-1.63375.3060.66820.8628-0.02550.4931-0.4183-0.0865-1.4139-1.3661-0.22970.4680.27660.03110.6940.01030.267633.273733.339921.8751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 2:105)B2 - 105
2X-RAY DIFFRACTION2(chain B and resid 106:132)B106 - 132
3X-RAY DIFFRACTION3(chain A and resid 3:121)A3 - 121
4X-RAY DIFFRACTION4(chain A and resid 122:139)A122 - 139

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