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- PDB-6k7e: Crystal structure of MBPapo-Tim21 fusion protein with a 17-residu... -

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Basic information

Entry
Database: PDB / ID: 6k7e
TitleCrystal structure of MBPapo-Tim21 fusion protein with a 17-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 import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / detection of maltose stimulus / maltose transport complex / 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: 1.534 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)56,7191
Polymers56,7191
Non-polymers00
Water14,178787
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 area23760 Å2
Unit cell
Length a, b, c (Å)156.807, 156.807, 67.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 56719.402 Da / Num. of mol.: 1 / Mutation: A313V
Source method: isolated from a genetically manipulated source
Details: MBPapo-Tim21 fusion protein with a 17-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.: 787 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M CaCl2, 0.1M HEPES, pH 7.0, 20% PEG 6000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 92372 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.118 / Net I/av σ(I): 17.13 / Net I/σ(I): 8.78
Reflection shellResolution: 1.53→1.56 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4565 / CC1/2: 0.691 / % 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: 1.534→39.202 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.1893 4494 4.87 %
Rwork0.1656 --
obs0.1667 92352 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.534→39.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 0 787 4700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194000
X-RAY DIFFRACTIONf_angle_d1.7195413
X-RAY DIFFRACTIONf_dihedral_angle_d13.831491
X-RAY DIFFRACTIONf_chiral_restr0.129587
X-RAY DIFFRACTIONf_plane_restr0.009700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5341-1.55150.33271710.27852892X-RAY DIFFRACTION99
1.5515-1.56980.27391330.2592929X-RAY DIFFRACTION100
1.5698-1.58890.30881440.23732912X-RAY DIFFRACTION100
1.5889-1.6090.23611430.22312972X-RAY DIFFRACTION100
1.609-1.63020.22011430.20062904X-RAY DIFFRACTION100
1.6302-1.65250.21351540.19452948X-RAY DIFFRACTION100
1.6525-1.67610.24111320.1882927X-RAY DIFFRACTION100
1.6761-1.70120.22921740.18982922X-RAY DIFFRACTION100
1.7012-1.72770.23491790.18212938X-RAY DIFFRACTION100
1.7277-1.75610.22451450.20072896X-RAY DIFFRACTION100
1.7561-1.78640.26311550.19632909X-RAY DIFFRACTION100
1.7864-1.81880.22031640.18752945X-RAY DIFFRACTION100
1.8188-1.85380.21621380.17482945X-RAY DIFFRACTION100
1.8538-1.89170.19471730.17092904X-RAY DIFFRACTION100
1.8917-1.93280.22311700.16682942X-RAY DIFFRACTION100
1.9328-1.97770.1951560.17332924X-RAY DIFFRACTION100
1.9777-2.02720.18761700.16552925X-RAY DIFFRACTION100
2.0272-2.0820.19021620.16152892X-RAY DIFFRACTION100
2.082-2.14330.20161530.15882894X-RAY DIFFRACTION100
2.1433-2.21240.20111340.16242988X-RAY DIFFRACTION100
2.2124-2.29150.21471260.16812963X-RAY DIFFRACTION100
2.2915-2.38320.21491430.16712924X-RAY DIFFRACTION100
2.3832-2.49170.19661510.16992950X-RAY DIFFRACTION100
2.4917-2.6230.2091320.16582946X-RAY DIFFRACTION100
2.623-2.78730.19381200.1692953X-RAY DIFFRACTION100
2.7873-3.00250.18961460.16852950X-RAY DIFFRACTION100
3.0025-3.30450.16091340.15872927X-RAY DIFFRACTION100
3.3045-3.78230.16431540.1532941X-RAY DIFFRACTION100
3.7823-4.7640.14361510.13792944X-RAY DIFFRACTION100
4.764-39.21450.1951440.17132852X-RAY DIFFRACTION97
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)
10.8288-0.24980.34480.37220.01020.6012-0.0549-0.0718-0.02260.0230.04660.0725-0.0824-0.07410.00470.0760.01570.03210.06840.00480.0666-27.958121.9158-20.045
20.0314-0.12960.06060.0132-0.0543-0.0853-0.02930.08710.2125-0.0554-0.0192-0.1952-0.1025-0.0111-0.0010.23590.02190.00080.1197-0.00330.1842-27.314949.3169-21.7278
30.61780.1771-0.10720.35230.02820.3239-0.02560.1045-0.0204-0.0564-0.04980.21220.0508-0.0316-0.00340.16130.0547-0.040.116-0.0220.11-55.657657.4005-22.8245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 353 )
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 500 )

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