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- PDB-2qz5: Crystal Structure of the C-terminal domain of Aida -

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Basic information

Entry
Database: PDB / ID: 2qz5
TitleCrystal Structure of the C-terminal domain of Aida
ComponentsAxin interactor, dorsalization associated protein
KeywordsSIGNALING PROTEIN / LIPID BINDING PROTEIN / Aida / Developmental protein
Function / homology
Function and homology information


determination of ventral identity / negative regulation of determination of dorsal identity / dorsal/ventral pattern formation / negative regulation of JNK cascade / regulation of protein-containing complex assembly / negative regulation of protein-containing complex assembly / protein domain specific binding / cytoplasm
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZheng, L.S.
CitationJournal: To be Published
Title: Crystal Structure of the C-terminal domain of Aida
Authors: Zheng, L.S.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Axin interactor, dorsalization associated protein
B: Axin interactor, dorsalization associated protein


Theoretical massNumber of molelcules
Total (without water)35,7542
Polymers35,7542
Non-polymers00
Water1,47782
1
A: Axin interactor, dorsalization associated protein


Theoretical massNumber of molelcules
Total (without water)17,8771
Polymers17,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Axin interactor, dorsalization associated protein


Theoretical massNumber of molelcules
Total (without water)17,8771
Polymers17,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.707, 55.732, 86.993
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17877.088 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aida / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q8C4Q6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (AIDA_MOUSE, Q8C4Q6) SHOWS CONFLICT AT THIS POSITION: R -> K (IN REF. 1; ...THE FEATURE OF UNIPROT (AIDA_MOUSE, Q8C4Q6) SHOWS CONFLICT AT THIS POSITION: R -> K (IN REF. 1; BAE34358 AND 2; AAH04835)

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Hepes 7.5, 25% PEG 3350, 0.2M Li2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10666 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.316 / Num. unique all: 1508 / % possible all: 95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZQ

2qzq


Resolution: 2.6→32.17 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 959 -random
Rwork0.225 ---
all0.245 9632 --
obs0.234 9517 99 %-
Refinement stepCycle: LAST / Resolution: 2.6→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 0 82 2558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.009

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