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- PDB-2qzq: Crystal structure of C-terminal of Aida -

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Basic information

Entry
Database: PDB / ID: 2qzq
TitleCrystal structure of C-terminal of Aida
ComponentsAxin interactor, dorsalization associated protein
KeywordsSIGNALING PROTEIN / LIPID BINDING PROTEIN / beta sheet sandwich / Coiled coil
Function / homology
Function and homology information


determination of ventral identity / negative regulation of determination of dorsal identity / negative regulation of JUN kinase activity / negative regulation of JNK cascade / dorsal/ventral pattern formation / negative regulation of protein-containing complex assembly / phosphatidylinositol binding / membrane
Similarity search - Function
Axin interactor, dorsalization-associated protein, N-terminal / Axin interactor dorsalization-associated protein, C-terminal / Axin interactor, dorsalization-associated protein, N-terminal domain superfamily / Aida N-terminus / Axin interactor dorsalisation-associated protein, C-terminal / C2 Aida-type domain profile. / C2 domain / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Axin interactor, dorsalization-associated protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZheng, L.S. / Wu, J.W.
CitationJournal: To be Published
Title: Crystal structure of C-terminal of Aida
Authors: Zheng, L.S.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Axin interactor, dorsalization associated protein


Theoretical massNumber of molelcules
Total (without water)17,6361
Polymers17,6361
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.951, 54.951, 130.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Axin interactor, dorsalization associated protein / Axin interaction partner and dorsalization antagonist


Mass: 17636.301 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Aida / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PBN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.4
Details: 0.1 HEPES Na pH 7.4, 12% PEG 3350, 2% MPD, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→47.56 Å / Num. all: 18670 / Num. obs: 18670 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.8 % / Biso Wilson estimate: 24.233 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.064 / Net I/σ(I): 33.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 9 / Num. unique all: 2652 / Rsym value: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementResolution: 1.9→26.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.819 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1858 10.2 %RANDOM
Rwork0.193 ---
all0.197 18670 --
obs0.197 18158 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.999 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 144 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221263
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0081704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36124.28649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.417155
X-RAY DIFFRACTIONr_chiral_restr0.1030.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02907
X-RAY DIFFRACTIONr_nbd_refined0.2160.2520
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.212
X-RAY DIFFRACTIONr_mcbond_it0.9751.5789
X-RAY DIFFRACTIONr_mcangle_it1.29521253
X-RAY DIFFRACTIONr_scbond_it2.5943525
X-RAY DIFFRACTIONr_scangle_it3.5524.5451
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 134 -
Rwork0.22 1075 -
all-1209 -
obs--90.83 %

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