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- PDB-3ady: Crystal structure of DotD from Legionella -

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Basic information

Entry
Database: PDB / ID: 3ady
TitleCrystal structure of DotD from Legionella
ComponentsDotD
KeywordsPROTON TRANSPORT / 3-layer(bab) sandwich / MTH1598-like
Function / homologyDotD protein / DotD protein / DotD superfamily / DotD protein / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Beta / DotD
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsImada, K. / Nakano, N. / Kubori, T. / Kinoshita, M. / Nagai, H.
CitationJournal: Plos Pathog. / Year: 2010
Title: Crystal structure of Legionella DotD: insights into the relationship between type IVB and type II/III secretion systems
Authors: Nakano, N. / Kubori, T. / Kinoshita, M. / Imada, K. / Nagai, H.
History
DepositionJan 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DotD


Theoretical massNumber of molelcules
Total (without water)16,1921
Polymers16,1921
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.860, 103.860, 103.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein DotD


Mass: 16191.568 Da / Num. of mol.: 1 / Fragment: periplasmic fragment, residues 20 -163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: dotD, lpg2674 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZS45
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 8% PEG 8000, 0.1M CHES-NaOH, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2→42.41 Å / Num. all: 12739 / Num. obs: 12739 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 29.39 Å2 / Rsym value: 0.072 / Net I/σ(I): 19.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1830 / Rsym value: 0.352 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→36.72 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2399416.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 623 4.9 %RANDOM
Rwork0.225 ---
obs0.225 12727 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5225 Å2 / ksol: 0.327575 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 0 180 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 96 4.6 %
Rwork0.271 1990 -
obs-2086 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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