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- PDB-5az7: Crystal structure of MBP-Tom20 fusion protein with a 4-residue sp... -

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Basic information

Entry
Database: PDB / ID: 5az7
TitleCrystal structure of MBP-Tom20 fusion protein with a 4-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 / Up-down Bundle / Mainly Alpha
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: 1.96 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.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
A: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3712
Polymers48,0291
Non-polymers3421
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.109, 113.908, 125.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

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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: 48028.551 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A313V, C409S,A313V, C409S
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 1-369 Maltose binding protein, 370-373 Linker and 374-435 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.: 1
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.: 101 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 50% PEG 400, 0.1M Phosphate citrate (pH 4.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 30663 / % possible obs: 93.1 % / Redundancy: 6.14 % / Net I/σ(I): 14.6

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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: 1.96→42.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.497 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.24196 1563 5.1 %RANDOM
Rwork0.19625 ---
obs0.19861 29097 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.961 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 23 101 3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023483
X-RAY DIFFRACTIONr_bond_other_d0.0010.023346
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9784731
X-RAY DIFFRACTIONr_angle_other_deg0.96837746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29226.184152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66315594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.509156
X-RAY DIFFRACTIONr_chiral_restr0.1280.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
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_it2.7223.2811735
X-RAY DIFFRACTIONr_mcbond_other2.7043.281734
X-RAY DIFFRACTIONr_mcangle_it3.4634.9012167
X-RAY DIFFRACTIONr_mcangle_other3.4624.9022168
X-RAY DIFFRACTIONr_scbond_it4.3633.7421748
X-RAY DIFFRACTIONr_scbond_other4.3623.7421748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3785.4042565
X-RAY DIFFRACTIONr_long_range_B_refined7.84527.2034021
X-RAY DIFFRACTIONr_long_range_B_other7.85227.1554002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.957→2.008 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 69 -
Rwork0.298 1416 -
obs--61.85 %

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