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- PDB-6jg0: Crystal structure of the N-terminal domain single mutant (S92E) o... -

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Basic information

Entry
Database: PDB / ID: 6jg0
TitleCrystal structure of the N-terminal domain single mutant (S92E) of the human mitochondrial calcium uniporter fused with T4 lysozyme
ComponentsEndolysin,Calcium uniporter protein
KeywordsTRANSPORT PROTEIN / Calcium channel
Function / homology
Function and homology information


mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis ...mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / viral release from host cell by cytolysis / calcium channel complex / peptidoglycan catabolic process / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / glucose homeostasis / host cell cytoplasm / mitochondrial inner membrane / 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 / Phage lysozyme / Lysozyme domain superfamily / 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: 2.5 Å
AuthorsLee, Y. / Park, J. / Min, C.K. / Kang, J.Y. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Eom, S.H.
CitationJournal: To Be Published
Title: Crystal structure of calcium channel domain
Authors: Lee, Y. / Park, J. / Min, C.K. / Kang, J.Y. / Kim, T.G. / Yamamoto, T. / Kim, D.H. / Eom, S.H.
History
DepositionFeb 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 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
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: Endolysin,Calcium uniporter protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0223
Polymers29,8301
Non-polymers1922
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-9 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.943, 97.943, 61.514
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 / Lysis protein / Lysozyme / Muramidase


Mass: 29830.170 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A,S92E
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF LYSOZYME (1-161), LINKER GS, CALCIUM UNIPORTER PROTEIN (75-165), AND TAGS LEHHHHHH
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


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.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 5% 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: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11124 / % possible obs: 99.7 % / Redundancy: 4.8 % / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.619 / Num. unique obs: 586 / CC1/2: 0.607 / Rpim(I) all: 0.368 / Rrim(I) all: 0.727 / % possible all: 99.8

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Processing

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

2lzm

4xtb


Resolution: 2.5→42.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.92 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25903 615 5.2 %RANDOM
Rwork0.18796 ---
obs0.1917 11124 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.5→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 10 77 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192051
X-RAY DIFFRACTIONr_bond_other_d0.0010.022022
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9712773
X-RAY DIFFRACTIONr_angle_other_deg0.75434621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1015251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88323.12596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75315370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1291522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02478
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3614.7671010
X-RAY DIFFRACTIONr_mcbond_other5.3514.7651009
X-RAY DIFFRACTIONr_mcangle_it7.7757.151259
X-RAY DIFFRACTIONr_mcangle_other7.7747.1541260
X-RAY DIFFRACTIONr_scbond_it5.935.4411041
X-RAY DIFFRACTIONr_scbond_other5.795.421034
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6877.841503
X-RAY DIFFRACTIONr_long_range_B_refined11.47738.7792441
X-RAY DIFFRACTIONr_long_range_B_other11.47438.7442421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 52 -
Rwork0.288 824 -
obs--99.89 %

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