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- PDB-1tqd: Crystal structure of IIGP1: a paradigm for interferon inducible p... -

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Basic information

Entry
Database: PDB / ID: 1tqd
TitleCrystal structure of IIGP1: a paradigm for interferon inducible p47 resistance GTPases
Componentsinterferon-inducible GTPase
KeywordsSIGNALING PROTEIN / GTPase / Interferon gamma / dimer / immunology
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 / innate immune response / GTPase activity / GTP binding / endoplasmic reticulum membrane / identical protein binding / cytoplasm
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Interferon-inducible GTPase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å
AuthorsGhosh, A. / Uthaiah, R. / Howard, J. / Herrmann, C. / Wolf, E.
Citation
Journal: Mol.Cell / Year: 2004
Title: Crystal Structure of IIGP1; A Paradigm for Interferon-Inducible p47 Resistance GTPases
Authors: Ghosh, A. / Uthaiah, R. / Howard, J. / Herrmann, C. / Wolf, E.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: IIGP1, an interferon-gamma-inducible 47-kDa GTPase of the mouse, showing cooperative enzymatic activity and GTP-dependent multimerization
Authors: Uthaiah, R.C. / Praefcke, G.J.K. / Howard, J.C. / Herrmann, C.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: interferon-inducible GTPase
B: interferon-inducible GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5524
Polymers95,2612
Non-polymers2912
Water11,061614
1
A: interferon-inducible GTPase


Theoretical massNumber of molelcules
Total (without water)47,6311
Polymers47,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: interferon-inducible GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9223
Polymers47,6311
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.071, 93.670, 139.848
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 interferon-inducible GTPase / / IIGP1


Mass: 47630.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IIGP1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QZ85
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.6 Å3/Da / Density % sol: 57 % / Description: the file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 20000, MES, Ethanol, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.9786, 0.9789, 0.9184
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEFeb 1, 2002
ADSC QUANTUM 42CCDFeb 1, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED SiMADMx-ray1
2SAGITALLY FOCUSED SiSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97891
30.91841
40.9341
ReflectionResolution: 2.3→20 Å / Num. all: 97950 / Num. obs: 97950 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.091 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.245 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.3→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs.
RfactorNum. reflectionSelection details
Rfree0.258 8202 RANDOM
Rwork0.214 --
all0.239 93653 -
obs0.236 90283 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 17 614 6867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.32
LS refinement shellHighest resolution: 2.3 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.258 8202 -
Rwork0.214 --
obs-90283 98.8 %

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