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- PDB-3n6o: Crystal structure of the GEF and P4M domain of DrrA/SidM from Leg... -

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Basic information

Entry
Database: PDB / ID: 3n6o
TitleCrystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila
Componentsguanine nucleotide exchange factor
KeywordsSIGNALING PROTEIN / phosphatidylinositol-4-phosphate / membrane / GEF / Rab / LCV / P4M / RabGEF
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 / small GTPase binding / host cell cytoplasmic vesicle membrane / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSchoebel, S. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
CitationJournal: Embo Rep. / Year: 2010
Title: High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA.
Authors: Schoebel, S. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: guanine nucleotide exchange factor
B: guanine nucleotide exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,01810
Polymers70,2502
Non-polymers7698
Water3,135174
1
A: guanine nucleotide exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5095
Polymers35,1251
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: guanine nucleotide exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5095
Polymers35,1251
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.962, 75.375, 130.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein guanine nucleotide exchange factor


Mass: 35124.957 Da / Num. of mol.: 2 / Fragment: GEF and P4M domains (UNP residues 340-647)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia / Gene: DrrA, lpg2464 / Plasmid: pET19mod_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q5ZSQ3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 298 K / pH: 4.8
Details: 20% (w/v) PEG4000, 0.16 M ammonium sulfate, 0.1 M sodium acetate, 20% glycerol, pH 4.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 10.61 / Number: 284116 / Rmerge(I) obs: 0.278 / D res high: 2.7 Å / Num. obs: 38712 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2029.949294.810.087
152011610010.094
101554710010.087
81072710010.095
68204310010.175
56256210010.228
45581310010.19
3.54586410010.242
3.23.5548810010.323
3.13.2232610010.407
33.1263110010.474
2.93301710010.547
2.82.9347210010.61
2.72.8401410010.697
ReflectionResolution: 2.5→19.9 Å / Num. obs: 26358 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.03 Å2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.004data extraction
SHARPphasing
RefinementResolution: 2.5→19.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.7 / SU ML: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.236 1291 4.9 %
Rwork0.17 --
obs0.173 26298 99.8 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.76 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 40 174 4961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224853
X-RAY DIFFRACTIONr_bond_other_d0.0040.023335
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.986526
X-RAY DIFFRACTIONr_angle_other_deg1.23338214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40825.794214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86115956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5771520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025287
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02871
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8141.53007
X-RAY DIFFRACTIONr_mcbond_other0.1571.51221
X-RAY DIFFRACTIONr_mcangle_it1.65324826
X-RAY DIFFRACTIONr_scbond_it2.77231846
X-RAY DIFFRACTIONr_scangle_it4.7514.51697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å
RfactorNum. reflection% reflection
Rfree0.295 95 -
Rwork0.212 1813 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4266-0.002-0.59250.06940.09650.99160.02210.00530.03710.01980.00460.00230.02630.058-0.02670.01850.0250.01170.04450.01740.0081-22.9154-14.715912.341
20.61690.01360.9380.1899-0.04561.94790.00830.0523-0.0476-0.04140.0091-0.001-0.05120.0464-0.01730.0180.0005-0.00780.05120.00520.0109-40.321914.4529-11.8508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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