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- PDB-3wz4: Structure of the periplasmic domain of DotI (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 3wz4
TitleStructure of the periplasmic domain of DotI (crystal form I)
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 / SAD / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DotI
B: DotI
C: DotI
D: DotI
E: DotI
F: DotI
G: DotI
H: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,58340
Polymers125,8028
Non-polymers3,78232
Water22,6271256
1
A: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DotI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1985
Polymers15,7251
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.590, 207.577, 58.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein
DotI / IcmL protein


Mass: 15725.213 Da / Num. of mol.: 8 / 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
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1256 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M CAPS pH10.5, 40% MPD, 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 MX225HE / 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: 2.2→54 Å / Num. all: 88995 / Num. obs: 88995 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4 / Num. unique all: 12299 / % possible all: 94.6

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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: SAD / Resolution: 2.2→37.425 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2000 2.25 %RANDOM
Rwork0.1908 ---
obs0.1918 88906 98.21 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.607 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5948 Å2-0 Å20 Å2
2---3.0756 Å2-0 Å2
3---2.4808 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8514 0 256 1256 10026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038978
X-RAY DIFFRACTIONf_angle_d0.63512240
X-RAY DIFFRACTIONf_dihedral_angle_d17.3233174
X-RAY DIFFRACTIONf_chiral_restr0.0451397
X-RAY DIFFRACTIONf_plane_restr0.0021545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.26841330.2105578893
2.255-2.3160.2691370.2169595195
2.316-2.38410.30591380.2129600696
2.3841-2.46110.27221390.2108606097
2.4611-2.5490.23821420.202613198
2.549-2.6510.25371410.2025617798
2.651-2.77160.26031430.2039620999
2.7716-2.91770.26581440.2049624299
2.9177-3.10040.25731440.19436252100
3.1004-3.33970.22541450.18226288100
3.3397-3.67550.20131460.17346331100
3.6755-4.20680.19631460.15986363100
4.2068-5.29770.19181480.15896450100
5.2977-37.43070.24241540.22336658100

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