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- PDB-2d5g: Structure of ubiquitin fold protein R767E mutant -

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Basic information

Entry
Database: PDB / ID: 2d5g
TitleStructure of ubiquitin fold protein R767E mutant
ComponentsAxin-1AXIN1
KeywordsSIGNALING PROTEIN / UBIQUITIN FOLD
Function / homology
Function and homology information


Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / hemoglobin metabolic process / response to quercetin / head development ...Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / hemoglobin metabolic process / response to quercetin / head development / cell development / Ub-specific processing proteases / dorsal/ventral axis specification / axial mesoderm formation / axial mesoderm development / post-anal tail morphogenesis / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / nervous system process / dorsal/ventral pattern formation / I-SMAD binding / negative regulation of protein metabolic process / adult walking behavior / Wnt signalosome / regulation of canonical Wnt signaling pathway / erythrocyte homeostasis / nucleocytoplasmic transport / negative regulation of fat cell differentiation / negative regulation of Wnt signaling pathway / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / lateral plasma membrane / cytoplasmic microtubule organization / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / cell periphery / sensory perception of sound / positive regulation of JNK cascade / regulation of protein phosphorylation / protein catabolic process / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / : / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of peptidyl-serine phosphorylation / cell cortex / cytoplasmic vesicle / protein-containing complex assembly / in utero embryonic development / molecular adaptor activity / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / synapse / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Ribosomal Protein L25; Chain P / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShibata, N. / Higuchi, Y.
CitationJournal: to be published
Title: Structure of ubiquitin fold protein R767E mutant
Authors: Shibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y.
History
DepositionNov 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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: Axin-1
B: Axin-1
C: Axin-1
D: Axin-1
E: Axin-1
F: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82516
Polymers58,8196
Non-polymers2,00610
Water0
1
A: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2043
Polymers9,8031
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2043
Polymers9,8031
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2043
Polymers9,8031
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0042
Polymers9,8031
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0042
Polymers9,8031
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2043
Polymers9,8031
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.550, 125.550, 115.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Axin-1 / AXIN1 / Axis inhibition protein 1 / rAxin


Mass: 9803.242 Da / Num. of mol.: 6 / Fragment: DIX DOMAIN / Mutation: R767E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PMALC2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: O70239
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Hg

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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: 2.98 Å3/Da / Density % sol: 58.66 % / Description: the file contains Friedel pairs.
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG8000, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 21930 / Num. obs: 21930 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 321432.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2081 9.5 %RANDOM
Rwork0.228 ---
all0.238 ---
obs0.238 21930 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.6075 Å2 / ksol: 0.281879 e/Å3
Displacement parametersBiso mean: 76.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å23.44 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 10 0 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.711.5
X-RAY DIFFRACTIONc_mcangle_it12.322
X-RAY DIFFRACTIONc_scbond_it16.292
X-RAY DIFFRACTIONc_scangle_it21.352.5
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.469 210 10.1 %
Rwork0.381 1868 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4pcmb.parampcmb.to

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