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- PDB-3sok: Dichelobacter nodosus pilin FimA -

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Basic information

Entry
Database: PDB / ID: 3sok
TitleDichelobacter nodosus pilin FimA
ComponentsFimbrial protein
KeywordsCELL ADHESION / pilus subunit / extracellular
Function / homology
Function and homology information


pilus / cell adhesion
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type IV major fimbrial protein FimA
Similarity search - Component
Biological speciesDichelobacter nodosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsArvai, A.S. / Craig, L. / Hartung, S. / Wood, T. / Kolappan, S. / Shin, D.S. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ultrahigh Resolution and Full-length Pilin Structures with Insights for Filament Assembly, Pathogenic Functions, and Vaccine Potential.
Authors: Hartung, S. / Arvai, A.S. / Wood, T. / Kolappan, S. / Shin, D.S. / Craig, L. / Tainer, J.A.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)32,2162
Polymers32,2162
Non-polymers00
Water1,09961
1
A: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)16,1081
Polymers16,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)16,1081
Polymers16,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.729, 105.729, 73.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Fimbrial protein / 198 antigen / Pilin / Serogroup A1


Mass: 16108.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dichelobacter nodosus (bacteria) / Gene: fimA / Plasmid: pJSM202 / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): PAK / References: UniProt: P02975
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 60% saturated ammonium sulfate 5% saturated NaCl 100mM Na Citrate 5% 1M NaPO4, pH 9.23, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2008
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→47.3 Å / Num. all: 39396 / Num. obs: 27380 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.52 Å / % possible all: 97.1

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 2HI2 conserved core (residues 1-55 + 78-92 + 105-111)

2hi2


Resolution: 2.3→47.283 Å / SU ML: 0.85 / σ(F): 1 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2902 1817 9.84 %RANDOM 10%
Rwork0.2337 ---
all0.2393 19139 --
obs0.2393 18469 96.51 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.362 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8569 Å2-0 Å20 Å2
2---1.8569 Å2-0 Å2
3---3.7137 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 0 61 2266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082221
X-RAY DIFFRACTIONf_angle_d1.0982990
X-RAY DIFFRACTIONf_dihedral_angle_d17.862816
X-RAY DIFFRACTIONf_chiral_restr0.078346
X-RAY DIFFRACTIONf_plane_restr0.004384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.38341340.25361202X-RAY DIFFRACTION93
2.3622-2.43170.36191340.24331232X-RAY DIFFRACTION95
2.4317-2.51020.35011550.251228X-RAY DIFFRACTION97
2.5102-2.59990.35131340.24991246X-RAY DIFFRACTION96
2.5999-2.7040.34191270.27481290X-RAY DIFFRACTION97
2.704-2.8270.37271300.26481278X-RAY DIFFRACTION97
2.827-2.97610.32831370.26751287X-RAY DIFFRACTION98
2.9761-3.16250.33811340.251308X-RAY DIFFRACTION99
3.1625-3.40660.25771560.2491305X-RAY DIFFRACTION98
3.4066-3.74930.31511360.22931286X-RAY DIFFRACTION97
3.7493-4.29150.23681390.20711280X-RAY DIFFRACTION95
4.2915-5.40560.24011470.19671337X-RAY DIFFRACTION98
5.4056-47.29340.28921540.2441373X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -21.7093 Å / Origin y: 0.0057 Å / Origin z: 12.6855 Å
111213212223313233
T0.1371 Å2-0.0541 Å2-0.0236 Å2-0.2392 Å20.0538 Å2--0.2295 Å2
L0.1562 °2-0.2869 °20.062 °2-0.5494 °20.0571 °2--0.5624 °2
S0.1082 Å °-0.0255 Å °-0.0392 Å °-0.0372 Å °-0.0544 Å °-0.3049 Å °0.0139 Å °0.0527 Å °0.0019 Å °
Refinement TLS groupSelection details: all

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