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- PDB-5uay: The structure of the Arabidopsis thaliana Toc75 POTRA domains -

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Basic information

Entry
Database: PDB / ID: 5uay
TitleThe structure of the Arabidopsis thaliana Toc75 POTRA domains
ComponentsProtein TOC75-3, chloroplastic
KeywordsMEMBRANE PROTEIN / POTRA / chloroplast
Function / homology
Function and homology information


Toc complex / TOC-TIC supercomplex I / protein targeting to chloroplast / protein import into chloroplast stroma / chloroplast organization / protein-transporting ATPase activity / plant-type vacuole / embryonic morphogenesis / chloroplast envelope / plastid ...Toc complex / TOC-TIC supercomplex I / protein targeting to chloroplast / protein import into chloroplast stroma / chloroplast organization / protein-transporting ATPase activity / plant-type vacuole / embryonic morphogenesis / chloroplast envelope / plastid / chloroplast / intracellular protein transport / cytosol
Similarity search - Function
Chloroplast envelope protein translocase, IAP75 / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Protein TOC75-3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsO'Neil, P.K. / Noinaj, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI113078-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2RO1-GM061893 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The POTRA domains of Toc75 exhibit chaperone-like function to facilitate import into chloroplasts.
Authors: O'Neil, P.K. / Richardson, L.G.L. / Paila, Y.D. / Piszczek, G. / Chakravarthy, S. / Noinaj, N. / Schnell, D.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TOC75-3, chloroplastic


Theoretical massNumber of molelcules
Total (without water)36,1381
Polymers36,1381
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.289, 54.773, 135.040
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 Protein TOC75-3, chloroplastic / 75 kDa translocon at the outer-envelope-membrane of chloroplasts 3 / AtTOC75-III


Mass: 36137.758 Da / Num. of mol.: 1 / Fragment: POTRA domains (UNP residues 141-449)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TOC75-3, TOC75, At3g46740, T6H20.230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9STE8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES:NaOH, pH7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13243 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.62 / Rsym value: 0.11 / Net I/σ(I): 33.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.62 / Rsym value: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→28.739 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2515 2421 9.95 %
Rwork0.1991 --
obs0.2045 24336 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 0 17 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082317
X-RAY DIFFRACTIONf_angle_d1.2233138
X-RAY DIFFRACTIONf_dihedral_angle_d15.607849
X-RAY DIFFRACTIONf_chiral_restr0.046360
X-RAY DIFFRACTIONf_plane_restr0.006412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4966-2.54750.34631260.33391160X-RAY DIFFRACTION89
2.5475-2.60290.4381430.31691324X-RAY DIFFRACTION100
2.6029-2.66340.38921380.32161264X-RAY DIFFRACTION100
2.6634-2.72990.34411510.29491333X-RAY DIFFRACTION100
2.7299-2.80370.30221360.29841260X-RAY DIFFRACTION100
2.8037-2.88610.30531470.2811317X-RAY DIFFRACTION100
2.8861-2.97920.36211430.26171289X-RAY DIFFRACTION100
2.9792-3.08550.30681530.24981312X-RAY DIFFRACTION100
3.0855-3.20890.3051440.24771290X-RAY DIFFRACTION100
3.2089-3.35470.37081420.24131298X-RAY DIFFRACTION100
3.3547-3.53130.26721440.23861288X-RAY DIFFRACTION100
3.5313-3.75210.24181420.21221304X-RAY DIFFRACTION100
3.7521-4.04110.25531400.19411284X-RAY DIFFRACTION100
4.0411-4.44640.23211420.17281305X-RAY DIFFRACTION100
4.4464-5.08680.19811500.15231284X-RAY DIFFRACTION100
5.0868-6.39710.2031360.17341306X-RAY DIFFRACTION100
6.3971-28.74130.21041440.14951297X-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)
18.8792-2.39520.23846.79761.16056.372-0.6205-0.1346-0.60630.19880.5225-0.78210.35331.09510.11430.6330.08590.16470.9301-0.14970.738414.679117.490442.4862
28.91562.91743.14383.90082.15189.0876-0.03480.9148-0.7517-0.62130.2540.41660.7984-0.6902-0.16130.7205-0.0956-0.00220.7419-0.09280.6537-10.119827.562945.6302
34.68161.69730.26136.14511.07497.4483-0.01410.76940.2966-0.91440.0572-0.1345-0.74080.3892-0.05210.6121-0.02130.11540.49910.02040.38952.187538.322949.571
46.98721.04153.47295.1534-0.24575.90550.2736-0.5454-0.86890.4830.0172-0.39410.7235-0.0768-0.33470.6965-0.0721-0.08240.47250.07050.52610.857228.372377.7581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 364 )
4X-RAY DIFFRACTION4chain 'A' and (resid 365 through 449 )

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