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- PDB-6k7d: Crystal structure of MBPapo-Tim21 fusion protein with a 16-residu... -

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Basic information

Entry
Database: PDB / ID: 6k7d
TitleCrystal structure of MBPapo-Tim21 fusion protein with a 16-residue helical linker
ComponentsMaltose/maltodextrin-binding periplasmic protein,Mitochondrial import inner membrane translocase subunit TIM21
KeywordsSUGAR BINDING PROTEIN / TRANSLOCASE / MBP / Tim21 / fusion protein / helical linker
Function / homology
Function and homology information


TIM23 mitochondrial import inner membrane translocase complex / protein insertion into mitochondrial inner membrane / 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 ...TIM23 mitochondrial import inner membrane translocase complex / protein insertion into mitochondrial inner membrane / 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 / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / mitochondrial inner membrane / DNA damage response / mitochondrion / membrane
Similarity search - Function
Mitochondrial import inner membrane translocase subunit Tim21 / Mitochondrial import inner membrane translocase subunit Tim21 / Tim21 IMS domain superfamily / TIM21 / 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 / Nuclear Transport Factor 2; Chain: A, ...Mitochondrial import inner membrane translocase subunit Tim21 / Mitochondrial import inner membrane translocase subunit Tim21 / Tim21 IMS domain superfamily / TIM21 / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Mitochondrial import inner membrane translocase subunit TIM21
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBala, S. / Shimada, A. / Kohda, D.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119002 Japan
Japan Society for the Promotion of ScienceJP19H05452 Japan
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.
Authors: Bala, S. / Shinya, S. / Srivastava, A. / Ishikawa, M. / Shimada, A. / Kobayashi, N. / Kojima, C. / Tama, F. / Miyashita, O. / Kohda, D.
History
DepositionJun 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Mitochondrial import inner membrane translocase subunit TIM21


Theoretical massNumber of molelcules
Total (without water)56,6481
Polymers56,6481
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23870 Å2
Unit cell
Length a, b, c (Å)47.010, 88.840, 119.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Mitochondrial import inner membrane translocase subunit TIM21 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 56648.324 Da / Num. of mol.: 1 / Mutation: A313V
Source method: isolated from a genetically manipulated source
Details: MBPapo-Tim21 fusion protein with a 16-residue helical linker
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: malE, b4034, JW3994, TIM21, YGR033C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: P53220
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MMT, pH 6.0, 24% PEG 1500 (w/v), 0.01M Betaine hydrochloride (additive)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34759 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.118 / Net I/av σ(I): 15.33 / Net I/σ(I): 10.03
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 1709 / CC1/2: 0.736 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000714data reduction
HKL-2000714data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PEB, 2CIU

1peb

2ciu


Resolution: 2→41.631 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.42
RfactorNum. reflection% reflection
Rfree0.229 1743 5.02 %
Rwork0.1754 --
obs0.1781 34697 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 0 319 4245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074013
X-RAY DIFFRACTIONf_angle_d1.0975429
X-RAY DIFFRACTIONf_dihedral_angle_d14.2061499
X-RAY DIFFRACTIONf_chiral_restr0.078588
X-RAY DIFFRACTIONf_plane_restr0.005702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0530.27841420.22592567X-RAY DIFFRACTION94
2.053-2.11920.27791250.21182719X-RAY DIFFRACTION100
2.1192-2.1950.2391480.19722702X-RAY DIFFRACTION100
2.195-2.28290.23971530.19132720X-RAY DIFFRACTION100
2.2829-2.38670.25931330.18342739X-RAY DIFFRACTION100
2.3867-2.51260.24411340.18162748X-RAY DIFFRACTION100
2.5126-2.670.2311500.17712734X-RAY DIFFRACTION100
2.67-2.87610.25381510.18822735X-RAY DIFFRACTION100
2.8761-3.16540.2371500.18612773X-RAY DIFFRACTION100
3.1654-3.62320.22061560.17292770X-RAY DIFFRACTION100
3.6232-4.5640.19251520.14512803X-RAY DIFFRACTION100
4.564-41.6310.22211490.16932944X-RAY DIFFRACTION99
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)
12.2345-0.10090.60510.9274-0.26761.4082-0.0013-0.0336-0.0417-0.08690.0224-0.0720.00590.031-0.02430.1834-0.02280.04810.115-0.01550.1853-14.00344.35530.2574
2-0.0113-0.3456-0.19450.4788-0.38770.3118-0.0294-0.0953-0.05650.00810.07480.04480.0809-0.0532-0.05260.2394-0.0257-0.02340.21170.03690.2674-28.4966-6.08950.4318
31.22050.3281-0.22131.9579-0.27942.1035-0.06330.27920.3157-0.06060.14790.0835-0.1462-0.2996-0.07190.27470.05960.03090.3880.09990.2277-26.6258-31.955522.6591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 315 )
2X-RAY DIFFRACTION2chain 'A' and (resid 316 through 398 )
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 500 )

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