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- PDB-5h54: Mdm12 from K. lactis 1-239 -

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Basic information

Entry
Database: PDB / ID: 5h54
TitleMdm12 from K. lactis 1-239
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


ERMES complex / protein insertion into mitochondrial outer membrane / phospholipid transport / mitochondrion-endoplasmic reticulum membrane tethering / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
Maintenance of mitochondrial morphology protein 1 / Mitochondrial distribution and morphology protein 12 / Mitochondrial distribution and morphology protein 12 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile.
Similarity search - Domain/homology
Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKawano, S. / Quinbara, S. / Endo, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25840020 Japan
CitationJournal: J. Cell Biol. / Year: 2018
Title: Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES
Authors: Kawano, S. / Tamura, Y. / Kojima, R. / Bala, S. / Asai, E. / Michel, A.H. / Kornmann, B. / Riezman, I. / Riezman, H. / Sakae, Y. / Okamoto, Y. / Endo, T.
History
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 20, 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: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)29,5001
Polymers29,5001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10660 Å2
Unit cell
Length a, b, c (Å)136.899, 136.899, 76.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Mitochondrial distribution and morphology protein 12 / Mitochondrial inheritance component MDM12


Mass: 29499.641 Da / Num. of mol.: 1 / Fragment: UNP residues 1-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: MDM12, KLLA0C06028g / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUC3

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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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Na-malate pH 7.0, 15-20% PEG3400, 0.1M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 1608644 / % possible obs: 99.8 % / Redundancy: 39.9 % / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.847 / SU B: 17.581 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 0.81 / ESU R Free: 0.435 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30745 371 4.6 %RANDOM
Rwork0.25283 ---
obs0.25528 7709 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 0 1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191577
X-RAY DIFFRACTIONr_bond_other_d0.0020.021480
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9822148
X-RAY DIFFRACTIONr_angle_other_deg0.84333382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7875200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.24225.44168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.63715252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.17157
X-RAY DIFFRACTIONr_chiral_restr0.080.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
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_it5.2247.752812
X-RAY DIFFRACTIONr_mcbond_other5.167.751811
X-RAY DIFFRACTIONr_mcangle_it7.93311.5941008
X-RAY DIFFRACTIONr_mcangle_other7.93311.5981009
X-RAY DIFFRACTIONr_scbond_it5.3057.979765
X-RAY DIFFRACTIONr_scbond_other5.2747.975763
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2111.8621140
X-RAY DIFFRACTIONr_long_range_B_refined11.64761.71796
X-RAY DIFFRACTIONr_long_range_B_other11.64461.7221797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 24 -
Rwork0.244 566 -
obs--99.83 %

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