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- PDB-5vkz: Crystal structure of Mdm12 and combinatorial reconstitution of Md... -

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Basic information

Entry
Database: PDB / ID: 5vkz
TitleCrystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID TRANSPORT / MDM12 / ERMES COMPLEX / SMP DOMAIN
Function / homology
Function and homology information


ERMES complex / mitochondrial genome maintenance / lipid transport / protein insertion into mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane
Similarity search - Function
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsEgea, P.F. / AhYoung, A.P. / Lu, B. / Tan, H.R. / Cascio, D.
Citation
Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies.
Authors: AhYoung, A.P. / Lu, B. / Cascio, D. / Egea, P.F.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly.
Authors: AhYoung, A.P. / Jiang, J. / Zhang, J. / Khoi Dang, X. / Loo, J.A. / Zhou, Z.H. / Egea, P.F.
#2: Journal: EMBO Rep. / Year: 2016
Title: Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex.
Authors: Jeong, H. / Park, J. / Lee, C.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / 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


Theoretical massNumber of molelcules
Total (without water)62,4442
Polymers62,4442
Non-polymers00
Water00
1
A: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)31,2221
Polymers31,2221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)31,2221
Polymers31,2221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.020, 116.020, 161.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 15 - 263 / Label seq-ID: 15 - 263

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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Components

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


Mass: 31222.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: AWRI1631 / Gene: MDM12, AWRI1631_151520 / Plasmid: pCDF / Details (production host): PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: B5VRP4

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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: 5.11 Å3/Da / Density % sol: 75.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15-25% PEG 3350, 400 mM ammonium phosphate, 3.5 mM Mega-10
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.1→85.3 Å / Num. obs: 10272 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 143.06 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.4
Reflection shellResolution: 4.1→4.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2 / Num. unique obs: 744 / CC1/2: 0.958 / Rsym value: 0.981 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GYD
Resolution: 4.1→85.34 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.945 / SU B: 49.37 / SU ML: 0.547 / Cross valid method: THROUGHOUT / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25379 1026 10 %RANDOM
Rwork0.24187 ---
obs0.24308 9220 99.53 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 263.699 Å2
Baniso -1Baniso -2Baniso -3
1-10.55 Å25.28 Å20 Å2
2--10.55 Å2-0 Å2
3----34.23 Å2
Refinement stepCycle: 1 / Resolution: 4.1→85.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 0 3424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.994731
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50225.192156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9421516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212560
X-RAY DIFFRACTIONr_gen_planes_other
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_it19.15526.2561707
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it29.67239.3732125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it22.81126.2151780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined40.84713811
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13108 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 4.1→4.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 73 -
Rwork0.475 663 -
obs--99.73 %

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