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- PDB-3etw: Crystal Structure of bacterial adhesin FadA -

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Basic information

Entry
Database: PDB / ID: 3etw
TitleCrystal Structure of bacterial adhesin FadA
ComponentsAdhesin A
KeywordsCELL ADHESION / antiparallel helix-loop-helix / Leucine chain / cell adhesin
Function / homologyAdhesion protein FadA / Adhesion protein FadA / Helix Hairpins - #1700 / : / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / THIOCYANATE ION / Adhesion A
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNithianantham, S. / Xu, M. / Wu, N. / Shoham, M. / Han, Y.W.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain.
Authors: Nithianantham, S. / Xu, M. / Yamada, M. / Ikegami, A. / Shoham, M. / Han, Y.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum
Authors: Nithianantham, S. / Xu, M. / Wu, N. / Han, Y.W. / Shoham, M.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionDec 2, 2008ID: 2AVR
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Adhesin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,6701
Non-polymers581
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 59.340, 126.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Adhesin A


Mass: 13669.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: fadA / Plasmid: pET21(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5I6B0
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 4.7 Å3/Da / Density % sol: 73.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate pH 5.6, 0.5M potassium thiocyanate, 5% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.0332
SYNCHROTRONALS 4.2.220.92871, 0.91999, 0.91979
Detector
TypeIDDetectorDateDetails
SBC-21CCDAug 3, 20053 x 3 mosaic
NOIR-12CCDJan 14, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal (Si-111)SINGLE WAVELENGTHMx-ray1
2Double crystal (Si-111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.928711
30.919991
40.919791
ReflectionResolution: 2→29.7 Å / Num. all: 17075 / Num. obs: 15871 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.677
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.813 / Num. unique all: 1068 / Χ2: 0.475 / % possible all: 63

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.92871.83-5.03
13 wavelength20.924.52-9.96
13 wavelength30.91984.75-9.01
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Br600.1480.3790.1631.178
2Br17.8450.2680.3260.1390.415
3Br27.3080.2630.3220.0140.647
4Br10.4280.4610.3180.1390.309

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.7 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.796 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1563 9.2 %Random
Rwork0.225 ---
all0.251 17075 --
obs0.247 15819 93 %-
Solvent computationBsol: 58.706 Å2
Displacement parametersBiso max: 88.12 Å2 / Biso mean: 49.109 Å2 / Biso min: 29.19 Å2
Baniso -1Baniso -2Baniso -3
1-12.055 Å22.459 Å20 Å2
2--12.055 Å20 Å2
3----24.111 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 3 162 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_mcbond_it1.9851.5
X-RAY DIFFRACTIONc_scbond_it3.6872
X-RAY DIFFRACTIONc_mcangle_it2.7752
X-RAY DIFFRACTIONc_scangle_it5.6252.5
LS refinement shellResolution: 2→2.02 Å /
RfactorNum. reflection
Rfree0.312 28
Rwork0.338 -
obs-278
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2scn.paramscn.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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