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- PDB-6k1z: Crystal structure of farnesylated hGBP1 -

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Basic information

Entry
Database: PDB / ID: 6k1z
TitleCrystal structure of farnesylated hGBP1
ComponentsGuanylate-binding protein 1
KeywordsHYDROLASE / GBP farnesylation
Function / homology
Function and homology information


GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptosis / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptosis / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. ...Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FARNESYL / Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsDu, S. / Xiao, J.Y.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural mechanism for guanylate-binding proteins (GBPs) targeting by the Shigella E3 ligase IpaH9.8.
Authors: Ji, C. / Du, S. / Li, P. / Zhu, Q. / Yang, X. / Long, C. / Yu, J. / Shao, F. / Xiao, J.Y.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3722
Polymers68,1661
Non-polymers2061
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.184, 113.959, 127.475
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 Guanylate-binding protein 1 / GTP-binding protein 1 / HuGBP-1 / Guanine nucleotide-binding protein 1 / Interferon-induced ...GTP-binding protein 1 / HuGBP-1 / Guanine nucleotide-binding protein 1 / Interferon-induced guanylate-binding protein 1


Mass: 68165.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P32455, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.02M Citric acid/0.08M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 31599 / % possible obs: 99.5 % / Redundancy: 11.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Net I/σ(I): 28.45
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.043 / Num. unique obs: 31559 / CC1/2: 0.918 / Rpim(I) all: 0.349

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.307→45.072 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.53
RfactorNum. reflection% reflection
Rfree0.2668 2000 8.06 %
Rwork0.2195 --
obs0.2234 24813 78.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.307→45.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 15 128 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034471
X-RAY DIFFRACTIONf_angle_d0.6116004
X-RAY DIFFRACTIONf_dihedral_angle_d3.1862783
X-RAY DIFFRACTIONf_chiral_restr0.039669
X-RAY DIFFRACTIONf_plane_restr0.005772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3071-2.36480.2824600.2657692X-RAY DIFFRACTION34
2.3648-2.42870.387710.2647809X-RAY DIFFRACTION40
2.4287-2.50020.3259820.2661938X-RAY DIFFRACTION46
2.5002-2.58090.367930.28711050X-RAY DIFFRACTION51
2.5809-2.67310.30151130.27541279X-RAY DIFFRACTION62
2.6731-2.78010.30951370.2761575X-RAY DIFFRACTION77
2.7801-2.90660.30251580.25881812X-RAY DIFFRACTION88
2.9066-3.05980.31691800.25882044X-RAY DIFFRACTION99
3.0598-3.25150.28521830.24922087X-RAY DIFFRACTION100
3.2515-3.50240.29471820.23072070X-RAY DIFFRACTION100
3.5024-3.85470.25891810.2072077X-RAY DIFFRACTION100
3.8547-4.41210.24181850.18172097X-RAY DIFFRACTION99
4.4121-5.55720.2161820.18312089X-RAY DIFFRACTION98
5.5572-45.08020.22111930.18822194X-RAY DIFFRACTION97

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