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- PDB-5az9: Crystal structure of (5-residue deleted)MBP-Tom20 fusion protein ... -

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Basic information

Entry
Database: PDB / ID: 5az9
TitleCrystal structure of (5-residue deleted)MBP-Tom20 fusion protein tethered with ALDH presequence via a disulfide bond
ComponentsMaltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
KeywordsSUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein Complex
Function / homology
Function and homology information


PINK1-PRKN Mediated Mitophagy / tRNA import into mitochondrion / response to 3,3',5-triiodo-L-thyronine / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / Ub-specific processing proteases / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity / mitochondrial envelope ...PINK1-PRKN Mediated Mitophagy / tRNA import into mitochondrion / response to 3,3',5-triiodo-L-thyronine / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / Ub-specific processing proteases / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein-transporting ATPase activity / mitochondrial envelope / protein targeting to mitochondrion / response to muscle activity / detection of maltose stimulus / maltose transport complex / protein import into mitochondrial matrix / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / sperm midpiece / ATP-binding cassette (ABC) transporter complex / cell periphery / cell chemotaxis / intracellular protein transport / unfolded protein binding / outer membrane-bounded periplasmic space / mitochondrial outer membrane / periplasmic space / DNA damage response / mitochondrion / membrane
Similarity search - Function
Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMatsuoka, R. / Kohda, D.
CitationJournal: Protein Sci. / Year: 2016
Title: Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.
Authors: Matsuoka, R. / Shimada, A. / Komuro, Y. / Sugita, Y. / Kohda, D.
History
DepositionSep 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
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: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog


Theoretical massNumber of molelcules
Total (without water)47,6291
Polymers47,6291
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.476, 71.396, 47.538
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog / MBP / MMBP / Maltodextrin-binding protein / Mitochondrial 20 kDa outer membrane protein / Outer ...MBP / MMBP / Maltodextrin-binding protein / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 47629.223 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A308V
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 1-364 Maltose binding protein, 365-368 Linker and 369-430 Tom20
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Rattus norvegicus (Norway rat)
Strain: K12 / Gene: malE, b4034, JW3994, Tomm20 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q62760
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 46512 / % possible obs: 99.8 % / Redundancy: 3.64 % / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 2V1T

1anf

2v1t


Resolution: 1.82→39.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.129 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22705 2351 5.1 %RANDOM
Rwork0.19209 ---
obs0.19391 44161 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.707 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.03 Å2
2---0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.82→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 0 172 3498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023403
X-RAY DIFFRACTIONr_bond_other_d0.0010.023288
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9724618
X-RAY DIFFRACTIONr_angle_other_deg0.95537605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68926.107149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47115589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.315156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
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_it3.1323.3781698
X-RAY DIFFRACTIONr_mcbond_other3.1333.3761697
X-RAY DIFFRACTIONr_mcangle_it4.2645.0432119
X-RAY DIFFRACTIONr_mcangle_other4.2645.0452120
X-RAY DIFFRACTIONr_scbond_it4.0653.8121703
X-RAY DIFFRACTIONr_scbond_other4.0643.8131704
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0275.5272499
X-RAY DIFFRACTIONr_long_range_B_refined7.47527.9234100
X-RAY DIFFRACTIONr_long_range_B_other7.46727.8454035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 152 -
Rwork0.282 3251 -
obs--99.77 %

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