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- PDB-3l0m: Crystal structure of Rab1-activation domain and P4M domain of Sid... -

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Basic information

Entry
Database: PDB / ID: 3l0m
TitleCrystal structure of Rab1-activation domain and P4M domain of SidM/DrrA from legionella
ComponentsDrrA
KeywordsPROTEIN BINDING / GEF/GDF of Rab1 / a new novel phosphatidylinositol 4-phosphate-binding domain
Function / homology
Function and homology information


: / protein guanylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / host cell cytoplasmic vesicle / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / regulation of GTPase activity / guanyl-nucleotide exchange factor activity ...: / protein guanylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / host cell cytoplasmic vesicle / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / regulation of GTPase activity / guanyl-nucleotide exchange factor activity / host cell cytoplasmic vesicle membrane / small GTPase binding / protein guanylyltransferase activity / extracellular region / ATP binding / membrane
Similarity search - Function
Monooxygenase - #280 / Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain ...Monooxygenase - #280 / Ferritin - #70 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / Monooxygenase / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Multifunctional virulence effector protein DrrA / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.45 Å
AuthorsZhu, Y. / Shao, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA
Authors: Zhu, Y. / Hu, L. / Zhou, Y. / Yao, Q. / Liu, L. / Shao, F.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DrrA
B: DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8584
Polymers76,6662
Non-polymers1922
Water0
1
A: DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4292
Polymers38,3331
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4292
Polymers38,3331
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.337, 144.337, 102.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DrrA / / SidM


Mass: 38332.902 Da / Num. of mol.: 2 / Fragment: Rab1-activation domain, P4M domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sidM / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q29ST3, UniProt: Q5ZSQ3*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 6.948323 Å3/Da / Density % sol: 82.29789 % / Mosaicity: 0.766 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.6M potassium sodium tartrate, 0.1M CHES, 0.1M Li2SO4, 0.1M sodium acetate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionRedundancy: 8.9 % / Number: 243624 / Rmerge(I) obs: 0.103 / Χ2: 2.19 / D res high: 3.45 Å / D res low: 20 Å / Num. obs: 27431 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.322092.110.0662.9838
5.867.3298.810.0873.1828.7
5.135.8699.510.0992.9558.8
4.675.1399.610.0912.5688.9
4.344.6799.710.1122.6528.9
4.094.3499.910.1582.1199
3.884.0910010.2231.7049.1
3.713.8810010.331.559.1
3.573.7199.910.5151.2859.1
3.453.5710010.9541.1469.1
ReflectionResolution: 3.449→144.337 Å / Num. all: 27736 / Num. obs: 27431 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.5→3.57 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.45→20 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2728 9.8 %RANDOM
Rwork0.214 ---
all0.217 27431 --
obs0.214 27365 98.8 %-
Solvent computationBsol: 106.393 Å2
Displacement parametersBiso max: 202.8 Å2 / Biso mean: 145.69 Å2 / Biso min: 71.52 Å2
Baniso -1Baniso -2Baniso -3
1--27.901 Å20 Å20 Å2
2---27.901 Å20 Å2
3---55.802 Å2
Refinement stepCycle: LAST / Resolution: 3.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 10 0 5119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007334
X-RAY DIFFRACTIONc_angle_deg1.3275
X-RAY DIFFRACTIONc_dihedral_angle_d20.71617
X-RAY DIFFRACTIONc_improper_angle_d0.79761
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2so4_xplor.param

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