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- PDB-3skq: Mdm38 is a 14-3-3-like receptor and associates with the protein s... -

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Basic information

Entry
Database: PDB / ID: 3skq
TitleMdm38 is a 14-3-3-like receptor and associates with the protein synthesis machinery at the inner mitochondrial membrane
ComponentsMitochondrial distribution and morphology protein 38
KeywordsMETAL TRANSPORT / 14-3-3-like membrane protein / mitochondrial ribosome / respiratory chain biogenesis / Letm1 homolog / 14-3-3 like fold / Ribosome binding receptor / Ribosomes / Mitochondrial inner membrane
Function / homology
Function and homology information


protein insertion into mitochondrial inner membrane from matrix / mitochondrial ribosome binding / positive regulation of mitochondrial translation / intracellular potassium ion homeostasis / proton transmembrane transport / potassium ion transport / mitochondrial inner membrane / mitochondrion
Similarity search - Function
LETM1-like, ribosome-binding domain / LETM1/MDM38-like / LETM1-like, RBD / Letm1 ribosome-binding (RBD) domain profile.
Similarity search - Domain/homology
IODIDE ION / : / Mitochondrial distribution and morphology protein 38
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLupo, D. / Tews, I. / Sinning, I.
CitationJournal: Traffic / Year: 2011
Title: Mdm38 is a 14-3-3-Like Receptor and Associates with the Protein Synthesis Machinery at the Inner Mitochondrial Membrane.
Authors: Lupo, D. / Vollmer, C. / Deckers, M. / Mick, D.U. / Tews, I. / Sinning, I. / Rehling, P.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,92710
Polymers28,8731
Non-polymers1,0549
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.527, 52.033, 47.232
Angle α, β, γ (deg.)90.00, 108.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3-

IOD

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Components

#1: Protein Mitochondrial distribution and morphology protein 38


Mass: 28873.141 Da / Num. of mol.: 1 / Fragment: C-terminal fragment, UNP residues 160-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MDM38, YOL027C / Plasmid: pGEX4t3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus R (DE3) -Ril / References: UniProt: Q08179
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.25M KI and 21% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 44933 / Num. obs: 16561 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.051 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 3.11 / Num. unique all: 2141 / Rsym value: 0.405 / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 831 5.02 %Random
Rwork0.1947 ---
all0.1964 44933 --
obs0.1964 16560 97.97 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.288 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2477 Å20 Å2-4.9634 Å2
2--9.9026 Å20 Å2
3----7.6549 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 9 149 2007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081881
X-RAY DIFFRACTIONf_angle_d0.9672526
X-RAY DIFFRACTIONf_dihedral_angle_d13.263731
X-RAY DIFFRACTIONf_chiral_restr0.071279
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.33091330.26712599X-RAY DIFFRACTION98
2.2316-2.40390.28971350.22952628X-RAY DIFFRACTION98
2.4039-2.64580.27841400.23012613X-RAY DIFFRACTION99
2.6458-3.02850.26211230.19612638X-RAY DIFFRACTION98
3.0285-3.81520.2111460.17872629X-RAY DIFFRACTION99
3.8152-42.86860.1791540.17132622X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.639-0.5080.47311.4613-0.92681.7898-0.0931-0.22050.79490.2603-0.2923-0.3176-0.32130.4594-0.26550.2833-0.0077-0.05410.1668-0.10210.240247.200419.685120.1424
20.39-0.54180.3370.9451-0.17690.96090.1220.64370.0754-0-0.0947-0.24330.21970.6376-0.02910.23660.12520.03640.38130.00220.213653.33844.1719-0.1542
31.48020.07840.6791.4046-0.17831.36720.0147-0.17060.02430.1384-0.1554-0.10450.00880.08240.03320.16050.03130.00170.1486-0.01990.17945.746910.185311.1934
41.02850.04810.01961.3567-0.16121.24560.2133-0.3213-0.33870.21930.00230.33630.1252-0.3789-0.05360.2073-0.02970.03150.24320.01060.238932.26634.120717.9688
50.7021-0.00240.18450.4792-0.03080.2797-0.0879-0.15440.08640.32190.00320.5384-0.3091-0.35190.05030.21720.09150.0780.4099-0.0580.330624.109817.326515.3595
60.6101-0.15970.08020.4253-0.25740.7527-0.0701-0.06590.2121-0.14550.13750.0383-0.3076-0.23940.01090.22250.06430.00020.1912-0.01620.292329.568718.45219.5037
71.108-0.18650.43920.2649-0.4040.78090.04560.27270.0989-0.01470.09740.09850.0175-0.03210.01720.15920.00780.0130.13890.0070.181539.527511.33588.9213
81.25460.42530.11450.6581-0.6430.96720.07260.14570.26830.28090.2784-0.0075-0.47620.18980.11670.485-0.10540.09310.45120.08230.422649.810124.28317.5491
91.1858-0.09460.95970.9655-0.51221.38-0.05670.33910.1916-0.2143-0.21080.091-0.23510.21640.0730.1770.0485-0.02240.2298-0.01510.200435.5520.911-8.3317
100.3590.63940.00781.114-0.0931.4207-0.0191-0.18310.2992-0.1053-0.0469-0.1664-0.05530.15850.0520.19030.00450.02510.16320.00210.186245.364515.35933.6501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 182:200)
2X-RAY DIFFRACTION2chain 'A' and (resseq 201:227)
3X-RAY DIFFRACTION3chain 'A' and (resseq 228:276)
4X-RAY DIFFRACTION4chain 'A' and (resseq 277:301)
5X-RAY DIFFRACTION5chain 'A' and (resseq 302:318)
6X-RAY DIFFRACTION6chain 'A' and (resseq 319:342)
7X-RAY DIFFRACTION7chain 'A' and (resseq 343:358)
8X-RAY DIFFRACTION8chain 'A' and (resseq 359:367)
9X-RAY DIFFRACTION9chain 'A' and (resseq 368:382)
10X-RAY DIFFRACTION10chain 'A' and (resseq 383:408)

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