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- PDB-1wsp: Crystal structure of axin dix domain -

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Basic information

Entry
Database: PDB / ID: 1wsp
TitleCrystal structure of axin dix domain
ComponentsAxin 1 proteinAXIN1
KeywordsSIGNALING PROTEIN
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 / Wnt signalosome / adult walking behavior / regulation of canonical Wnt signaling pathway / erythrocyte homeostasis / nucleocytoplasmic transport / negative regulation of protein metabolic process / 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
BENZOIC ACID / : / : / Axin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsShibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y.
CitationJournal: to be published
Title: Crystal structure of axin dix domain
Authors: Shibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y.
History
DepositionNov 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Axin 1 protein
B: Axin 1 protein
C: Axin 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,13013
Polymers29,2033
Non-polymers1,92710
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.130, 92.130, 85.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsEach one of the chains (A, B, and C) is the minimum biological unit.

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Components

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


Mass: 9734.206 Da / Num. of mol.: 3 / Fragment: DIX DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMALc2 / Production host: Escherichia coli (E. coli) / References: GenBank: 2982198, UniProt: O70239*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.33 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 7.5 / Details: PEG8000, pH 7.5, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→58.772 Å / Num. all: 9245 / Num. obs: 9237 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 157 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1335 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.17 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1214210.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 963 10.5 %RANDOM
Rwork0.246 ---
obs0.246 9206 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.362 Å2 / ksol: 0.326264 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å22.37 Å20 Å2
2--1.14 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 18 204 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d23.4
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_it5.931.5
X-RAY DIFFRACTIONc_mcangle_it8.822
X-RAY DIFFRACTIONc_scbond_it13.182
X-RAY DIFFRACTIONc_scangle_it14.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.463 109 11.9 %
Rwork0.313 807 -
obs--100 %
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.TOP

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