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- PDB-7zgi: chloroplast trigger factor (TIG1) -

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Basic information

Entry
Database: PDB / ID: 7zgi
Titlechloroplast trigger factor (TIG1)
ComponentsPeptidylprolyl isomerase
KeywordsCHAPERONE / Molecular chaperones / chloroplast / co-translational folding / PPIase
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / : / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / peptidylprolyl isomerase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsCarius, Y. / Ries, F. / Gries, K. / Trentmann, O. / Willmund, F. / Lancaster, C.R.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural features of chloroplast trigger factor determined at 2.6 angstrom resolution.
Authors: Carius, Y. / Ries, F. / Gries, K. / Trentmann, O. / Lancaster, C.R.D. / Willmund, F.
History
DepositionApr 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidylprolyl isomerase
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,29414
Polymers109,1012
Non-polymers1,19312
Water46826
1
A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0516
Polymers54,5511
Non-polymers5005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2438
Polymers54,5511
Non-polymers6937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.291, 69.879, 106.043
Angle α, β, γ (deg.)90.000, 110.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein Peptidylprolyl isomerase / Chloroplast trigger factor (TIG1)


Mass: 54550.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TIG1, CHLRE_01g001750v5, CHLREDRAFT_196868 / Production host: Escherichia coli K12 (bacteria) / Strain (production host): ER2556 / References: UniProt: A8JD56, peptidylprolyl isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3 M MgSO4, 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 2.6→54.31 Å / Num. obs: 37064 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.548 / Num. unique obs: 4515 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→54.31 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 1738 4.7 %RANDOM
Rwork0.235 ---
obs0.2371 35263 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.53 Å2 / Biso mean: 57.871 Å2 / Biso min: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å2-2.19 Å2
2--5.68 Å20 Å2
3----1.52 Å2
Refinement stepCycle: final / Resolution: 2.6→54.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 68 26 5301
Biso mean--65.84 39.68 -
Num. residues----656
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 144 -
Rwork0.354 2560 -
all-2704 -
obs--99.3 %

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