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- PDB-1dg3: STRUCTURE OF HUMAN GUANYLATE BINDING PROTEIN-1 IN NUCLEOTIDE FREE FORM -

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Basic information

Entry
Database: PDB / ID: 1dg3
TitleSTRUCTURE OF HUMAN GUANYLATE BINDING PROTEIN-1 IN NUCLEOTIDE FREE FORM
ComponentsPROTEIN (INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1)
KeywordsSIGNALING PROTEIN / GBP / GTP HYDROLYSIS / GDP / GMP / INTERFERON INDUCED / DYNAMIN RELATED / LARGE GTPASE FAMILY
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
Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPrakash, B. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C.
Citation
Journal: Nature / Year: 2000
Title: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins.
Authors: Prakash, B. / Praefcke, G.J. / Renault, L. / Wittinghofer, A. / Herrmann, C.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Nucleotide-Binding Characteristics of Human Guanylate-Binding Protein 1(Hgbp1) and Identification of the Third GTP-Binding Motif
Authors: Praefcke, G.J.K. / Geyer, M. / Schwemmle, M. / Kalbitzer, H.R. / Herrmann, C.
History
DepositionNov 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)68,0041
Polymers68,0041
Non-polymers00
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.470, 41.030, 121.000
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1) / GUANINE NUCLEOTIDE- BINDING PROTEIN 1


Mass: 68003.594 Da / Num. of mol.: 1 / Fragment: FULL LENGTH PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32455
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100MM MES-NAOH, 7.5% PEG6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
25 %PEG60001reservoir
3100 mMMes-NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. obs: 66520 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.06
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.299 / % possible all: 95.1
Reflection shell
*PLUS
% possible obs: 95.1 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
CCP4model building
DMmodel building
CNSrefinement
XDSdata scaling
CCP4phasing
DMphasing
RefinementResolution: 1.8→29.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 20880635.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: STRUCTURE DETERMINED BY MIR
RfactorNum. reflection% reflectionSelection details
Rfree0.276 6722 10.1 %RANDOM
Rwork0.242 ---
obs0.242 66520 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.22 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.31 Å20 Å2-2.28 Å2
2--3.21 Å20 Å2
3----9.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 0 341 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.051.5
X-RAY DIFFRACTIONc_mcangle_it3.912
X-RAY DIFFRACTIONc_scbond_it4.752
X-RAY DIFFRACTIONc_scangle_it6.692.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 1086 10.3 %
Rwork0.331 9487 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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