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- PDB-3wz5: Structure of the periplasmic domain of DotI (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 3wz5
TitleStructure of the periplasmic domain of DotI (crystal form II)
ComponentsDotI
KeywordsUNKNOWN FUNCTION / type IVB secretion
Function / homologyType-IV b secretion system, inner-membrane complex component / Type-IV b secretion system, inner-membrane complex component / membrane / DotI
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKuroda, T. / Kubori, T. / Uchida, Y. / Nagai, H. / Imada, K.
CitationJournal: Sci Rep / Year: 2015
Title: Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion
Authors: Kuroda, T. / Kubori, T. / Thanh Bui, X. / Hyakutake, A. / Uchida, Y. / Imada, K. / Nagai, H.
History
DepositionSep 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DotI
B: DotI
C: DotI
D: DotI


Theoretical massNumber of molelcules
Total (without water)62,9014
Polymers62,9014
Non-polymers00
Water00
1
A: DotI


Theoretical massNumber of molelcules
Total (without water)15,7251
Polymers15,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DotI


Theoretical massNumber of molelcules
Total (without water)15,7251
Polymers15,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DotI


Theoretical massNumber of molelcules
Total (without water)15,7251
Polymers15,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DotI


Theoretical massNumber of molelcules
Total (without water)15,7251
Polymers15,7251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)230.328, 230.328, 230.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein
DotI / IcmL protein


Mass: 15725.213 Da / Num. of mol.: 4 / Fragment: periplasmic domain, UNP residues 73-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: dotI, icmL / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O54626
Has protein modificationY

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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: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.2M NaCl, 40% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 35 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97923 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3.5→81.4 Å / Num. all: 13479 / Num. obs: 13479 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 16.7
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 10.4 / Num. unique all: 1913 / % possible all: 100

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Processing

Software
NameVersionClassification
SPring-8BBSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZ4

3wz4


Resolution: 3.5→72.836 Å / SU ML: 0.63 / σ(F): 1.5 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 665 4.94 %RANDOM
Rwork0.1794 ---
obs0.1812 13465 99.88 %-
all-13465 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.86 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→72.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 0 0 4178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044286
X-RAY DIFFRACTIONf_angle_d0.7355840
X-RAY DIFFRACTIONf_dihedral_angle_d15.1141518
X-RAY DIFFRACTIONf_chiral_restr0.046673
X-RAY DIFFRACTIONf_plane_restr0.003757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5003-3.77050.25111150.19872516100
3.7705-4.14990.2461350.17932504100
4.1499-4.75030.17331490.14752512100
4.7503-5.98450.22581200.17582577100
5.9845-72.85180.20661460.1982269199

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