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- PDB-4mxp: Structural Basis for PI(4)P-Specific Membrane Recruitment of the ... -

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Basic information

Entry
Database: PDB / ID: 4mxp
TitleStructural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM
ComponentsDefects in Rab1 recruitment protein A
KeywordsPI(4)P-BINDING PROTEIN / Protein-lipid complex / Guanine Nucleotide Exchange Factor / Rab1 binding
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
Chem-DB4 / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsDel Campo, C.M. / Mishra, A.K. / Wang, Y.H. / Roy, C.R. / Janmey, P.A. / Lambright, D.G.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM.
Authors: Del Campo, C.M. / Mishra, A.K. / Wang, Y.H. / Roy, C.R. / Janmey, P.A. / Lambright, D.G.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Defects in Rab1 recruitment protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6923
Polymers37,1141
Non-polymers5772
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.552, 128.552, 53.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Defects in Rab1 recruitment protein A / Multifunctional virulence effector protein DrrA / Adenosine monophosphate-protein transferase / ...Multifunctional virulence effector protein DrrA / Adenosine monophosphate-protein transferase / AMPylator / Guanosine monophosphate-protein transferase / GMPylator / Rab1 guanine nucleotide exchange factor


Mass: 37114.199 Da / Num. of mol.: 1 / Fragment: GEF and P4M domains, UNP residues 330-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: drrA, lpg2464, sidM / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZSQ3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-DB4 / (2R)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate


Mass: 554.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O16P2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4-6% PEG 3350, 100 mM Tris, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 10, 2010
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 38272 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.83→1.86 Å / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L0M

3l0m


Resolution: 1.83→26.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.266 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.114 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1906 5 %RANDOM
Rwork0.1886 ---
all0.1896 ---
obs0.1896 38240 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.79 Å2 / Biso mean: 27.0265 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.83→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 36 195 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192535
X-RAY DIFFRACTIONr_bond_other_d0.0050.022474
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9883409
X-RAY DIFFRACTIONr_angle_other_deg0.73535740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9225313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4125.752113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08515507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7091512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_mcbond_it1.5022.4421243
X-RAY DIFFRACTIONr_mcbond_other1.4982.441242
X-RAY DIFFRACTIONr_mcangle_it2.2733.6561553
LS refinement shellResolution: 1.83→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 --
Rwork0.239 2649 -
all-2787 -
obs-1734 92.8 %

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