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- PDB-5bz6: Crystal structure of the N-terminal domain single mutant (S92A) o... -

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Basic information

Entry
Database: PDB / ID: 5bz6
TitleCrystal structure of the N-terminal domain single mutant (S92A) of the human mitochondrial calcium uniporter fused with T4 lysozyme
ComponentsLysozyme,Calcium uniporter protein, mitochondrial
KeywordsTRANSPORT PROTEIN / Membrane protein / Calcium channel / Mitochondria
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 / peptidoglycan catabolic process / calcium channel complex / 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: 2.75 Å
AuthorsLee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. ...Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.-S. / Wang, J. / Kim, D.H. / Eom, S.H.
CitationJournal: Embo Rep. / Year: 2015
Title: Structure and function of the N-terminal domain of the human mitochondrial calcium uniporter.
Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / ...Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.S. / Wang, J. / Kim, D.H. / Eom, S.H.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Other
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Dec 25, 2019Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_struct_oper_list
Item: _entity.pdbx_fragment / _entity_name_com.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 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: Lysozyme,Calcium uniporter protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3497
Polymers29,7721
Non-polymers5766
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.803, 97.803, 61.537
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 Lysozyme,Calcium uniporter protein, mitochondrial / Lysis protein / Muramidase / HsMCU / Coiled-coil domain-containing protein 109A


Mass: 29772.135 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A, S1092A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of bacteriophage T4 lysozyme protein (UNP RESIDUES 1-163), LINKER GS, anmitochondrial calcium uniporter N-terminal domain (UNP RESIDUES 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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1M Bis-Tris-HCl (pH 6.5), 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 11171 / % possible obs: 99.47 % / Redundancy: 4.7 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LZM, 4XSJ

2lzm

4xsj


Resolution: 2.75→34.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.522 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 410 4.8 %RANDOM
Rwork0.164 ---
obs0.167 8147 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.75→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 30 41 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192063
X-RAY DIFFRACTIONr_bond_other_d0.0020.022021
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9792792
X-RAY DIFFRACTIONr_angle_other_deg0.98134617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68223.05395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5971522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it2.353.1131010
X-RAY DIFFRACTIONr_mcbond_other2.3513.111009
X-RAY DIFFRACTIONr_mcangle_it3.8724.6651259
X-RAY DIFFRACTIONr_mcangle_other3.8714.6681260
X-RAY DIFFRACTIONr_scbond_it3.3243.6891053
X-RAY DIFFRACTIONr_scbond_other3.2053.6441030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5075.2551498
X-RAY DIFFRACTIONr_long_range_B_refined8.25525.1222319
X-RAY DIFFRACTIONr_long_range_B_other8.13125.1222315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 20 -
Rwork0.205 465 -
obs--75.43 %

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