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- PDB-5az6: Crystal structure of MBP-Tom20 fusion protein with a 2-residue sp... -

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Basic information

Entry
Database: PDB / ID: 5az6
TitleCrystal structure of MBP-Tom20 fusion protein with a 2-residue spacer in the connector helix
ComponentsMaltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
KeywordsSUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / 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: 2.56 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
A: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4054
Polymers95,7212
Non-polymers6852
Water37821
1
B: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2032
Polymers47,8601
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2032
Polymers47,8601
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.906, 81.227, 109.890
Angle α, β, γ (deg.)90.00, 106.38, 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: 47860.379 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A313V
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 1-369 Maltose binding protein, 370-371 Linker, and 372-433 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 16% PEG 3350, 0.2M Disodium malonate, 0.1M HEPES (pH7.3)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 35889 / % possible obs: 99.9 % / Redundancy: 3.79 % / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 2V1T

1anf

2v1t


Resolution: 2.56→24.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.48 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25972 1784 5 %RANDOM
Rwork0.20337 ---
obs0.20625 34036 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.19 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.56→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 46 21 6821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026958
X-RAY DIFFRACTIONr_bond_other_d0.0040.026692
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9789450
X-RAY DIFFRACTIONr_angle_other_deg1.124315476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7055864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0326.184304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.447151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1311512
X-RAY DIFFRACTIONr_chiral_restr0.0960.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217846
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021462
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_it3.9665.8143462
X-RAY DIFFRACTIONr_mcbond_other3.9635.8133461
X-RAY DIFFRACTIONr_mcangle_it5.9728.7144324
X-RAY DIFFRACTIONr_mcangle_other5.9738.7154325
X-RAY DIFFRACTIONr_scbond_it4.1396.1783496
X-RAY DIFFRACTIONr_scbond_other4.1386.1783497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2619.0795127
X-RAY DIFFRACTIONr_long_range_B_refined9.7447.17923
X-RAY DIFFRACTIONr_long_range_B_other9.73947.0997924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.56→2.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 104 -
Rwork0.271 2321 -
obs--93.38 %

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