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- PDB-4ytv: Crystal structure of Mdm35 -

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Basic information

Entry
Database: PDB / ID: 4ytv
TitleCrystal structure of Mdm35
ComponentsMitochondrial distribution and morphology protein 35
KeywordsPROTEIN BINDING / Disulfide bond / Mitochondria
Function / homology
Function and homology information


TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / mitochondrial respiratory chain complex assembly / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
: / Mitochondrial distribution and morphology protein 35
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsWatanabe, Y. / Tamura, Y. / Kawano, S. / Endo, T.
CitationJournal: Nat Commun / Year: 2015
Title: Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria.
Authors: Watanabe, Y. / Tamura, Y. / Kawano, S. / Endo, T.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5663
Polymers9,4151
Non-polymers1512
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.144, 59.144, 123.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein Mitochondrial distribution and morphology protein 35


Mass: 9414.575 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: O60200
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M MES pH 6.5, 1.2 M Ammonium sulfate, 10 mM Cobalt(II) chloride

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.0, 0.97919, 0.97932, 0.96426
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979191
30.979321
40.964261
ReflectionResolution: 1.45→50 Å / Num. obs: 15031 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 68.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 18 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
PHENIXmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.45→29.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 135559.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1499 10.2 %RANDOM
Rwork0.197 ---
obs0.197 14681 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5406 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2--2.13 Å20 Å2
3----4.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.04 Å
Refinement stepCycle: 1 / Resolution: 1.45→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 7 72 621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.205 237 10.3 %
Rwork0.211 2060 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top
X-RAY DIFFRACTION6CNS_TOPPAR/glycerol.paramCNS_TOPPAR/glycerol.top

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