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- PDB-6k7f: Crystal structure of MBPholo-Tim21 fusion protein with a 17-resid... -

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Basic information

Entry
Database: PDB / ID: 6k7f
TitleCrystal structure of MBPholo-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 / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity ...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 / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / mitochondrial inner membrane / periplasmic space / DNA damage response / mitochondrion / membrane
Similarity search - Function
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
Similarity search - Domain/homology
alpha-maltose / 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: 1.8 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 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 22, 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/maltodextrin-binding periplasmic protein,Mitochondrial import inner membrane translocase subunit TIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9912
Polymers55,6481
Non-polymers3421
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint2 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.970, 69.410, 171.360
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: 55648.258 Da / Num. of mol.: 1 / Mutation: A313V
Source method: isolated from a genetically manipulated source
Details: MBPholo-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: 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 / Water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M K/Na Tartrate, 16% PEG 3350 (w/v), microseeds

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46285 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.26
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.02 / Num. unique obs: 7366 / CC1/2: 0.885 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 2CIU

1anf

2ciu


Resolution: 1.8→35.282 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 2313 5 %
Rwork0.1745 --
obs0.1766 46239 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 23 319 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014033
X-RAY DIFFRACTIONf_angle_d1.3175458
X-RAY DIFFRACTIONf_dihedral_angle_d13.5961510
X-RAY DIFFRACTIONf_chiral_restr0.096597
X-RAY DIFFRACTIONf_plane_restr0.006701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.83720.30621330.27752541X-RAY DIFFRACTION99
1.8372-1.87720.26631350.24572564X-RAY DIFFRACTION100
1.8772-1.92080.29911330.24372523X-RAY DIFFRACTION100
1.9208-1.96890.31181340.22582543X-RAY DIFFRACTION100
1.9689-2.02210.29451340.21922543X-RAY DIFFRACTION100
2.0221-2.08160.31071330.20892539X-RAY DIFFRACTION100
2.0816-2.14880.27971360.1942569X-RAY DIFFRACTION100
2.1488-2.22560.24491340.18872548X-RAY DIFFRACTION100
2.2256-2.31470.24161360.19152570X-RAY DIFFRACTION100
2.3147-2.420.24391340.19852560X-RAY DIFFRACTION100
2.42-2.54750.24971360.19832577X-RAY DIFFRACTION100
2.5475-2.70710.24841360.19332583X-RAY DIFFRACTION100
2.7071-2.9160.2781370.2022589X-RAY DIFFRACTION100
2.916-3.20930.23071370.19282606X-RAY DIFFRACTION100
3.2093-3.67330.18981380.16112622X-RAY DIFFRACTION100
3.6733-4.62630.18861400.13892662X-RAY DIFFRACTION100
4.6263-35.28890.15521470.14872787X-RAY DIFFRACTION100
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)
11.9934-0.8781-0.30592.43330.35481.8288-0.0951-0.11210.11090.17660.05390.181-0.1857-0.14630.02950.18110.0437-0.05890.2051-0.02650.19182.9706-4.6784-16.1075
21.029-0.4429-2.21141.36082.32737.9371-0.1192-0.02910.36130.05510.07370.0042-0.45240.02680.01760.36440.0414-0.09460.25890.01530.44558.482913.363-35.284
31.7888-0.44931.34761.8972-0.3624.2325-0.1031-0.168-0.0916-0.03460.06250.0711-0.1612-0.08130.07150.255-0.04890.02310.21780.06080.293811.5332-1.6298-54.7101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 357 )
2X-RAY DIFFRACTION2chain 'A' and (resid 358 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 499 )

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