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- PDB-6kir: High resolution structure of mouse CXorf40A -

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Basic information

Entry
Database: PDB / ID: 6kir
TitleHigh resolution structure of mouse CXorf40A
ComponentsUncharacterized protein CXorf40 homolog
KeywordsIMMUNE SYSTEM / PUA-like / ASCH domain / Chromosome X / mitochondria
Function / homologyProtein EOLA1/EOLA2 / ASCH / ASCH domain / ASCH domain / PUA-like superfamily / Protein EOLA1
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsWu, B.X.
CitationJournal: To Be Published
Title: High resolution structure of mouse CXorf40A
Authors: Wu, B.X.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein CXorf40 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4713
Polymers18,2791
Non-polymers1922
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.252, 50.943, 96.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-404-

HOH

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Components

#1: Protein Uncharacterized protein CXorf40 homolog


Mass: 18278.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D1F3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate, 2% Polyethylene glycol 400, 0.1 M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97736 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97736 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 24456 / % possible obs: 99.7 % / Redundancy: 21.1 % / Net I/σ(I): 38.9
Reflection shellResolution: 1.55→1.61 Å / Num. unique obs: 2333

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→27.86 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.247 --
Rwork0.181 --
obs-23168 99.66 %
Refinement stepCycle: LAST / Resolution: 1.55→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 10 104 1383

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