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- PDB-4lv5: Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI -

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Basic information

Entry
Database: PDB / ID: 4lv5
TitleMurine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI
Components
  • Interferon-inducible GTPase 1
  • Rhoptry protein 5B
KeywordsTransferase/Hydrolase / immune related GTPase / guanine dissociation inhibitor / parasite effector / Transferase-Hydrolase complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / protein kinase activity / innate immune response / GTPase activity / GTP binding / endoplasmic reticulum membrane / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Immunity-related GTPases-like / IRG-type guanine nucleotide-binding (G) domain / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Immunity-related GTPases-like / IRG-type guanine nucleotide-binding (G) domain / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / Rhoptry protein 5B / Interferon-inducible GTPase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsReese, M.L. / Boothroyd, J.C.
CitationJournal: To be Published
Title: Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI
Authors: Reese, M.L. / Shah, N. / Boothroyd, J.C.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Derived calculations
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Rhoptry protein 5B
B: Interferon-inducible GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,02411
Polymers89,7032
Non-polymers1,3219
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhoptry protein 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9727
Polymers41,2181
Non-polymers7546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Interferon-inducible GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0524
Polymers48,4841
Non-polymers5673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 54.700, 85.600
Angle α, β, γ (deg.)99.000, 106.600, 106.900
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Rhoptry protein 5B / / Type I rhoptry protein 5 / Type I rhoptry protein 5B / Type III rhoptry protein 5


Mass: 41218.145 Da / Num. of mol.: 1 / Fragment: UNP residues 175-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ROP5, ROP5B / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2YGR7
#2: Protein Interferon-inducible GTPase 1 /


Mass: 48484.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Iigp1, Irga6 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9QZ85, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 492 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.1M Ammonium Citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→39.33 Å / Num. obs: 92554 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.613 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.19
Reflection shell

Rmerge(I) obs: 0.018 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.741.1552192686099.6
1.74-1.791.5251272661399.4
1.79-1.841.9754267658099.7
1.84-1.92.6651643626699.9
1.9-1.963.5650035617299.6
1.96-2.034.8547296592299.7
2.03-2.116.0742732567499.3
2.11-2.198.5145043552999.7
2.19-2.2910.7744056528599.8
2.29-2.413.1241562502299.8
2.4-2.5316.0839316477799.5
2.53-2.6920.1334966448798.6
2.69-2.8726.434970427499.2
2.87-3.134.4933477392599.7
3.1-3.447.1430587364699.8
3.4-3.861.2126382327698.8
3.8-4.3975.1222744288198.7
4.39-5.3885.1921173247799.7
5.38-7.676.3614889186098.4
7.6113.18909102898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8_1069refinement
XSCALEdata scaling
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q60 and then 1TPZ:A using phaser

3q60

1tpz


Resolution: 1.7→39.328 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 1.97 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 4650 5.03 %
Rwork0.1923 --
obs0.1941 92476 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.77 Å2 / Biso mean: 38.0282 Å2 / Biso min: 17.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 83 483 6519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086307
X-RAY DIFFRACTIONf_angle_d1.1068554
X-RAY DIFFRACTIONf_chiral_restr0.078963
X-RAY DIFFRACTIONf_plane_restr0.0051092
X-RAY DIFFRACTIONf_dihedral_angle_d14.4252385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.40781600.36712913307399
1.7193-1.73950.38391630.34052889305299
1.7395-1.76080.34831670.33192928309599
1.7608-1.7830.35521670.32142895306299
1.783-1.80650.3291420.295429653107100
1.8065-1.83130.30361400.287229473087100
1.8313-1.85740.29751430.281329293072100
1.8574-1.88510.35351720.267130043176100
1.8851-1.91460.33121570.267228643021100
1.9146-1.9460.3231950.247629243119100
1.946-1.97950.30461500.24528863036100
1.9795-2.01550.28771500.23729873137100
2.0155-2.05430.31871610.229228993060100
2.0543-2.09620.26961430.22632961310499
2.0962-2.14180.22381470.212928773024100
2.1418-2.19160.24351470.20230233170100
2.1916-2.24640.26621400.199128903030100
2.2464-2.30720.25261640.20329353099100
2.3072-2.3750.22791580.197429643122100
2.375-2.45170.2251520.200729073059100
2.4517-2.53930.27281480.203729423090100
2.5393-2.6410.241480.19932922307099
2.641-2.76110.24651550.20042893304898
2.7611-2.90660.23681600.19729503110100
2.9066-3.08870.22741550.190529273082100
3.0887-3.32710.22661500.186829303080100
3.3271-3.66170.1971650.17329133078100
3.6617-4.1910.19011550.15872901305698
4.191-5.27820.17761580.146429433101100
5.2782-39.33810.18281380.17312918305699

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