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- PDB-3jz9: Crystal structure of the GEF domain of DrrA/SidM from Legionella ... -

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Basic information

Entry
Database: PDB / ID: 3jz9
TitleCrystal structure of the GEF domain of DrrA/SidM from Legionella pneumophila
ComponentsUncharacterized protein DrrA
KeywordsTRANSPORT PROTEIN / RabGDI / RabGEF / GDI / GEF / GDF / GDI displacement factor
Function / homology
Function and homology information


: / protein guanylylation / AMPylase activity / protein adenylylation / protein adenylyltransferase / 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 adenylylation / protein adenylyltransferase / 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
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 / Ferritin ...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 / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsSchoebel, S. / Oesterlin, L.K. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
Citation
Journal: Mol.Cell / Year: 2009
Title: RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity.
Authors: Schoebel, S. / Oesterlin, L.K. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
#1: Journal: Science / Year: 2007
Title: A bifunctional bacterial protein links GDI displacement to Rab1 activation.
Authors: Machner, M.P. / Isberg, R.R.
#2: Journal: Nature / Year: 2007
Title: Legionella pneumophila proteins that regulate Rab1 membrane cycling.
Authors: Ingmundson, A. / Delprato, A. / Lambright, D.G. / Roy, C.R.
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein DrrA


Theoretical massNumber of molelcules
Total (without water)22,3881
Polymers22,3881
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.338, 126.338, 35.925
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-34-

HOH

DetailsBiological unit is the same as asymmetric unit.

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Components

#1: Protein Uncharacterized protein DrrA


Mass: 22388.299 Da / Num. of mol.: 1 / Fragment: GEF domain: UNP residues 340-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / DSM 7513 / Gene: lpg2464 / Plasmid: pET19mod_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q5ZSQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.25 M Sodium sulfate, 21% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00749 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00749 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 30729 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.569 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.4624247754518199.3
1.9-20.3155.8206703690199.4
2-2.20.17310.2321595509199.7
2.2-2.50.1116.1329325333199.8
2.5-30.06425.2302484883199.9
3-3.50.03938.71512224511100
3.5-40.02851.4861814201100
4-50.02360.1862314041100
5-70.02358.45754950199.9
7-100.01771.321473661100
10-150.01476.8784139199.3
15-250.01969.1268521100
25-300.02381.93261100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
REFMAC5.5.0070phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→27.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.449 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1544 5 %RANDOM
Rwork0.169 ---
obs0.17 30721 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 225 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221592
X-RAY DIFFRACTIONr_bond_other_d0.0010.021093
X-RAY DIFFRACTIONr_angle_refined_deg2.3041.9692154
X-RAY DIFFRACTIONr_angle_other_deg1.21632705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66625.94269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.096156
X-RAY DIFFRACTIONr_chiral_restr0.1620.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
X-RAY DIFFRACTIONr_mcbond_it1.5021.51000
X-RAY DIFFRACTIONr_mcbond_other0.5381.5401
X-RAY DIFFRACTIONr_mcangle_it2.47321612
X-RAY DIFFRACTIONr_scbond_it4.4083592
X-RAY DIFFRACTIONr_scangle_it6.3444.5536
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 102 -
Rwork0.224 2125 -
all-2227 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 43.2328 Å / Origin y: 33.1224 Å / Origin z: 0.1269 Å
111213212223313233
T0.097 Å20.0711 Å2-0.0331 Å2-0.0655 Å2-0.0248 Å2--0.0601 Å2
L1.2947 °2-0.791 °20.3705 °2-1.0886 °2-0.3593 °2--0.144 °2
S0.0599 Å °0.0757 Å °-0.1005 Å °-0.0528 Å °-0.0266 Å °-0.0131 Å °0.0472 Å °0.0329 Å °-0.0333 Å °

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