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- PDB-6kit: Structure of mouse CXorf40A, Selenomethionine derivative -

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Basic information

Entry
Database: PDB / ID: 6kit
TitleStructure of mouse CXorf40A, Selenomethionine derivative
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: 1.57 Å
AuthorsWu, B.X.
CitationJournal: To Be Published
Title: Structure of mouse CXorf40A, Selenomethionine derivative
Authors: Wu, B.X.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)18,4654
Polymers18,1761
Non-polymers2883
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.128, 96.102, 33.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Uncharacterized protein CXorf40 homolog


Mass: 18176.461 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 23707 / % possible obs: 100 % / Redundancy: 12.7 % / Net I/σ(I): 22.21
Reflection shellResolution: 1.57→1.63 Å / Num. unique obs: 2320

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2174 --
Rwork0.1834 --
obs0.1851 22436 99.81 %
Refinement stepCycle: LAST / Resolution: 1.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 15 159 1443

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