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- PDB-4yvo: Crystal Structure of the TPR Domain of Arabidopsis FLU (FLU-TPR) -

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Basic information

Entry
Database: PDB / ID: 4yvo
TitleCrystal Structure of the TPR Domain of Arabidopsis FLU (FLU-TPR)
ComponentsProtein FLUORESCENT IN BLUE LIGHT, chloroplastic
KeywordsFLUORESCENT PROTEIN / TPR / chloroplast
Function / homology
Function and homology information


chloroplast membrane / chlorophyll biosynthetic process / chloroplast thylakoid membrane
Similarity search - Function
Protein FLUORESCENT IN BLUE LIGHT / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Protein FLUORESCENT IN BLUE LIGHT, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsZhang, M. / Zhang, F. / Liu, L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Non-canonical Tetratricopeptide Repeat (TPR) Domain of Fluorescent (FLU) Mediates Complex Formation with Glutamyl-tRNA Reductase.
Authors: Zhang, M. / Zhang, F. / Fang, Y. / Chen, X. / Chen, Y. / Zhang, W. / Dai, H.E. / Lin, R. / Liu, L.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Theoretical massNumber of molelcules
Total (without water)18,4261
Polymers18,4261
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.193, 60.193, 67.489
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Mass: 18425.977 Da / Num. of mol.: 1 / Fragment: TPR Domain (UNP RESIDUES 189-316)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FLU, At3g14110, MAG2.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q940U6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.2M NaCl, 0.1M Bis-tris pH6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 25072 / % possible obs: 98 % / Redundancy: 10.7 % / Net I/σ(I): 24.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RO3

3ro3


Resolution: 1.45→26.064 Å / FOM work R set: 0.903 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 1275 5.11 %
Rwork0.1403 23698 -
obs0.1421 24973 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.28 Å2 / Biso mean: 19.06 Å2 / Biso min: 6.95 Å2
Refinement stepCycle: final / Resolution: 1.45→26.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 0 151 1080
Biso mean---32.74 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051005
X-RAY DIFFRACTIONf_angle_d0.9421360
X-RAY DIFFRACTIONf_chiral_restr0.069150
X-RAY DIFFRACTIONf_plane_restr0.003177
X-RAY DIFFRACTIONf_dihedral_angle_d14.598406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4501-1.50810.19691340.12432320245487
1.5081-1.57680.16551300.10862491262194
1.5768-1.65990.14851460.104626552801100
1.6599-1.76390.16191250.111326802805100
1.7639-1.90.17181490.116326542803100
1.9-2.09110.16081410.125726962837100
2.0911-2.39360.16691620.129126822844100
2.3936-3.01490.19481630.155627162879100
3.0149-26.06850.181250.16462804292998

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