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- PDB-3qdh: Crystal structure of Actinomyces fimbrial adhesin FimA -

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Basic information

Entry
Database: PDB / ID: 3qdh
TitleCrystal structure of Actinomyces fimbrial adhesin FimA
ComponentsFimbrial structural subunit
KeywordsCELL ADHESION / isopeptide bonds / Actinomyces type 2 fimbriae / CnaA/DEv-IgG fold / CnaB/IgG-rev fold / Gram-positive bacterial cell wall protein / fimbrial structural subunit / CELL AHDESION / pilin
Function / homology
Function and homology information


membrane => GO:0016020 / metal ion binding
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbrial structural subunit
Similarity search - Component
Biological speciesActinomyces naeslundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsDevarajan, B. / Krishnan, V. / Narayana, S.V.L.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Two autonomous structural modules in the fimbrial shaft adhesin FimA mediate Actinomyces interactions with streptococci and host cells during oral biofilm development.
Authors: Mishra, A. / Devarajan, B. / Reardon, M.E. / Dwivedi, P. / Krishnan, V. / Cisar, J.O. / Das, A. / Narayana, S.V. / Ton-That, H.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial structural subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0832
Polymers31,0171
Non-polymers651
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.528, 39.799, 77.139
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein Fimbrial structural subunit


Mass: 31017.447 Da / Num. of mol.: 1 / Fragment: C-terminal domains, residues 199-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces naeslundii (bacteria) / Strain: T14V / Gene: fimA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68212
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 2000 MME, 0.1M imidazole, 0.2M zinc acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONAPS 24-ID-C20.979
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJun 11, 2009
ADSC QUANTUM 3152CCDDec 3, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
ReflectionResolution: 1.9→40 Å / Num. obs: 22677 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 11.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
autoSHARPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.709 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24902 1161 5.1 %RANDOM
Rwork0.20915 ---
obs0.21132 21483 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.09 Å2
2--0.48 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 1 199 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222078
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9762823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87625.97682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.754158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211539
X-RAY DIFFRACTIONr_mcbond_it0.5491.51350
X-RAY DIFFRACTIONr_mcangle_it1.04422191
X-RAY DIFFRACTIONr_scbond_it1.5813728
X-RAY DIFFRACTIONr_scangle_it2.7864.5631
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 85 -
Rwork0.26 1549 -
obs--99.03 %

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