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- PDB-6kvx: Crystal structure of the N-terminal domain single mutant (D119A) ... -

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Basic information

Entry
Database: PDB / ID: 6kvx
TitleCrystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme
ComponentsEndolysin,Calcium uniporter protein, mitochondrial
KeywordsTRANSPORT PROTEIN / MCU / mitochondrial calcium uniporter / Calcium channel
Function / homology
Function and homology information


uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission ...uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / cell wall macromolecule catabolic process / glucose homeostasis / protein complex oligomerization / lysozyme / lysozyme activity / mitochondrial inner membrane / host cell cytoplasm / defense response to bacterium / mitochondrion / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLee, Y. / Park, J. / Lee, G. / Yoon, S. / Min, C.K. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Lee, K.W. / Eom, S.H.
CitationJournal: Sci Rep / Year: 2020
Title: Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme
Authors: Lee, Y. / Park, J.S. / Kang, J.Y. / Eom, S.H.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin,Calcium uniporter protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9715
Polymers29,5871
Non-polymers3844
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.899, 97.899, 61.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Endolysin,Calcium uniporter protein, mitochondrial / Lysis protein / Lysozyme / Muramidase / HsMCU / Coiled-coil domain-containing protein 109A


Mass: 29586.928 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A,D119A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q8NE86, lysozyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) polyethylene glycol (PEG) 3350, 5% (v/v) glycerol, 0.3 M (NH4)2SO4, and 0.1 M Bis-Tris-HCl (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 7820 / % possible obs: 98.7 % / Redundancy: 4.2 % / CC1/2: 0.943 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.3
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 413 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LZM, 4XTB

2lzm

4xtb


Resolution: 2.85→28.96 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26218 400 5.1 %RANDOM
Rwork0.1795 ---
obs0.18357 7489 98.64 %-
Refinement stepCycle: LAST / Resolution: 2.85→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 20 0 2025
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 42 -
Rwork0.304 547 -
all-20 -
obs--99.83 %

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