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- PDB-5h5a: Mdm12 from K. lactis (1-239), Lys residues are uniformly dimethyl... -

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Basic information

Entry
Database: PDB / ID: 5h5a
TitleMdm12 from K. lactis (1-239), Lys residues are uniformly dimethyl modified
Components(Mitochondrial distribution and morphology protein 12) x 2
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


ERMES complex / mitochondrial genome maintenance / phospholipid transport / mitochondrion-endoplasmic reticulum membrane tethering / protein insertion into mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
MMM1 domain / Maintenance of mitochondrial morphology protein 1 / 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
Chem-6OU / : / Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKawano, S. / Quinbara, S. / Endo, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
apan 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 12
B: Mitochondrial distribution and morphology protein 12
C: Mitochondrial distribution and morphology protein 12
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,92712
Polymers111,8994
Non-polymers3,0288
Water36020
1
A: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2243
Polymers27,4661
Non-polymers7572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint0 kcal/mol
Surface area11410 Å2
MethodPISA
2
B: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2573
Polymers29,5001
Non-polymers7572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint1 kcal/mol
Surface area11600 Å2
MethodPISA
3
C: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2243
Polymers27,4661
Non-polymers7572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area11490 Å2
MethodPISA
4
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2243
Polymers27,4661
Non-polymers7572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint1 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.868, 48.524, 130.126
Angle α, β, γ (deg.)90.01, 91.50, 90.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 0 - 234

Dom-IDEns-IDAuth asym-IDLabel asym-IDLabel seq-ID
11AA1 - 235
21BB20 - 254
12AA1 - 235
22CC1 - 235
13AA1 - 235
23DD1 - 235
14BB20 - 254
24CC1 - 235
15BB20 - 254
25DD1 - 235
16CC1 - 235
26DD1 - 235

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 27466.426 Da / Num. of mol.: 3 / Fragment: UNP residues 1-239
Source method: isolated from a genetically manipulated source
Details: phosphatidylethanolamine
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-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUC3
#2: 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-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUC3
#3: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.26M NaH2PO4, 0.14M K2HPO4 pH 5.6

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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: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 527803 / % possible obs: 97.1 % / Redundancy: 3.8 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.647 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.258 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28615 2438 5.1 %RANDOM
Rwork0.2507 ---
obs0.25248 45717 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.304 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å2-0.41 Å2-0.53 Å2
2---1.42 Å2-0.51 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 200 20 6934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027026
X-RAY DIFFRACTIONr_bond_other_d0.010.026920
X-RAY DIFFRACTIONr_angle_refined_deg2.0032.0049471
X-RAY DIFFRACTIONr_angle_other_deg2.0733.01515958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96325.333315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.146151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511534
X-RAY DIFFRACTIONr_chiral_restr0.1070.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217629
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021469
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_it3.1144.0833370
X-RAY DIFFRACTIONr_mcbond_other3.1094.0823369
X-RAY DIFFRACTIONr_mcangle_it4.86.1024188
X-RAY DIFFRACTIONr_mcangle_other4.8016.1034189
X-RAY DIFFRACTIONr_scbond_it3.6784.5923656
X-RAY DIFFRACTIONr_scbond_other3.6784.5933657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7146.7155284
X-RAY DIFFRACTIONr_long_range_B_refined8.04432.7197439
X-RAY DIFFRACTIONr_long_range_B_other8.04432.7247440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119570.13
12B119570.13
21A114250.15
22C114250.15
31A113430.15
32D113430.15
41B113380.16
42C113380.16
51B113880.15
52D113880.15
61C110810.16
62D110810.16
LS refinement shellResolution: 2.252→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 167 -
Rwork0.373 3035 -
obs--87.34 %

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