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- PDB-4jw1: Crystal structure of N-terminal 618-residue fragment of LepB from... -

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Basic information

Entry
Database: PDB / ID: 4jw1
TitleCrystal structure of N-terminal 618-residue fragment of LepB from Legionella pneumophila
ComponentsEffector protein B
KeywordsHYDROLASE ACTIVATOR / New GAP fold / GTPase-Accelerating Protein / Rab1
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #830 / LepB GAP domain, C-terminal subdomain / LepB, N-terminal / LepB GAP domain, N-terminal subdomain / LepB GAP domain N-terminal subdomain / LepB GAP domain C-terminal subdomain / LepB N-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Effector protein B
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.16 Å
AuthorsHu, L. / Yao, Q. / Zhu, Y. / Shao, F.
CitationJournal: Cell Res. / Year: 2013
Title: Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP
Authors: Yu, Q. / Hu, L. / Yao, Q. / Zhu, Y. / Dong, N. / Wang, D.-C. / Shao, F.
History
DepositionMar 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Effector protein B
B: Effector protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4138
Polymers142,7632
Non-polymers6506
Water543
1
A: Effector protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6633
Polymers71,3821
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Effector protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7505
Polymers71,3821
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.536, 159.418, 181.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Effector protein B / GTPase-Activating Protein


Mass: 71381.633 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, UNP residues 1-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lepB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6X1Y7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.1M citrate, 20% MPEG 2000, pH 6.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. obs: 25525 / % possible obs: 99.5 % / Observed criterion σ(I): 13.5 / Biso Wilson estimate: 35.44 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.16→19.95 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7915 / SU ML: 0.33 / σ(F): 0 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 1269 5.01 %
Rwork0.264 --
obs0.2649 25323 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.54 Å2 / Biso mean: 43.1404 Å2 / Biso min: 4.58 Å2
Refinement stepCycle: LAST / Resolution: 3.16→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6691 0 43 3 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126857
X-RAY DIFFRACTIONf_angle_d1.1689216
X-RAY DIFFRACTIONf_chiral_restr0.0781019
X-RAY DIFFRACTIONf_plane_restr0.0061158
X-RAY DIFFRACTIONf_dihedral_angle_d17.7112524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.16-3.2860.2911400.22922553269397
3.286-3.43480.3031320.246726342766100
3.4348-3.61490.32561430.256826562799100
3.6149-3.83990.29871390.249826692808100
3.8399-4.1340.29691380.2426592797100
4.134-4.54550.29711390.227126922831100
4.5455-5.19310.25441450.235526892834100
5.1931-6.50490.28171440.291226982842100
6.5049-19.94990.28161490.28812804295399

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