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- PDB-4yvq: Crystal Structure of FLU-TPR in Complex with the C-terminal Regio... -

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Basic information

Entry
Database: PDB / ID: 4yvq
TitleCrystal Structure of FLU-TPR in Complex with the C-terminal Region of GluTR
Components
  • Glutamyl-tRNA reductase 1, chloroplastic
  • Protein FLUORESCENT IN BLUE LIGHT, chloroplastic
KeywordsOXIDOREDUCTASE/FLUORESCENT PROTEIN / TPR / chloroplast / protein-protein interaction / OXIDOREDUCTASE-FLUORESCENT PROTEIN complex
Function / homology
Function and homology information


glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / chloroplast membrane / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / chloroplast thylakoid membrane / chloroplast / NADP binding / protein-containing complex
Similarity search - Function
Protein FLUORESCENT IN BLUE LIGHT / Glutamyl-tRNA reductase / Glutamyl-tRNA reductase, N-terminal / Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain / Glutamyl-tRNA reductase, conserved site / Glutamyl-tRNA reductase, N-terminal domain superfamily / Glutamyl tRNA-reductase dimerization domain superfamily / Glutamyl-tRNAGlu reductase, dimerisation domain / Glutamyl-tRNAGlu reductase, N-terminal domain / Glutamyl-tRNA reductase signature. ...Protein FLUORESCENT IN BLUE LIGHT / Glutamyl-tRNA reductase / Glutamyl-tRNA reductase, N-terminal / Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain / Glutamyl-tRNA reductase, conserved site / Glutamyl-tRNA reductase, N-terminal domain superfamily / Glutamyl tRNA-reductase dimerization domain superfamily / Glutamyl-tRNAGlu reductase, dimerisation domain / Glutamyl-tRNAGlu reductase, N-terminal domain / Glutamyl-tRNA reductase signature. / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Glutamyl-tRNA reductase 1, chloroplastic / Protein FLUORESCENT IN BLUE LIGHT, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 / Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
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_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA reductase 1, chloroplastic
C: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Theoretical massNumber of molelcules
Total (without water)29,9132
Polymers29,9132
Non-polymers00
Water1,45981
1
A: Glutamyl-tRNA reductase 1, chloroplastic
C: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic

A: Glutamyl-tRNA reductase 1, chloroplastic
C: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Theoretical massNumber of molelcules
Total (without water)59,8274
Polymers59,8274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)74.735, 74.735, 161.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Glutamyl-tRNA reductase 1, chloroplastic / / GluTR


Mass: 12142.102 Da / Num. of mol.: 1 / Fragment: C-terminal Region (UNP RESIDUES 440-543)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HEMA1, HEMA, At1g58290, F19C14.9 / Production host: Escherichia coli (E. coli) / References: UniProt: P42804, glutamyl-tRNA reductase
#2: Protein Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Mass: 17771.264 Da / Num. of mol.: 1 / Fragment: TPR Domain (UNP RESIDUES 195-316)
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.15M KBr, 30% w/v Polyethylene glycol monomethyl ether 2000

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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: Nov 30, 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: 2.4→50 Å / Num. obs: 11100 / % possible obs: 99.9 % / Redundancy: 10.2 % / Net I/σ(I): 26.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YVO

4yvo


Resolution: 2.401→34.28 Å / FOM work R set: 0.8144 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 530 4.8 %
Rwork0.2079 10521 -
obs0.2095 11051 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.65 Å2 / Biso mean: 48.66 Å2 / Biso min: 22.42 Å2
Refinement stepCycle: final / Resolution: 2.401→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 0 81 1683
Biso mean---51.4 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041630
X-RAY DIFFRACTIONf_angle_d0.6752181
X-RAY DIFFRACTIONf_chiral_restr0.051244
X-RAY DIFFRACTIONf_plane_restr0.002278
X-RAY DIFFRACTIONf_dihedral_angle_d13.752640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4011-2.64270.28441290.230325282657
2.6427-3.02490.31931400.241225632703
3.0249-3.81030.23281410.217926122753
3.8103-34.28390.21311200.190528182938
Refinement TLS params.Method: refined / Origin x: 32.767 Å / Origin y: 39.4155 Å / Origin z: 5.3824 Å
111213212223313233
T0.3049 Å2-0 Å2-0.0423 Å2-0.3239 Å20.0906 Å2--0.3358 Å2
L2.1418 °20.5629 °2-0.1843 °2-2.4456 °2-0.6215 °2--2.4642 °2
S-0.2212 Å °0.0993 Å °0.4234 Å °-0.0184 Å °0.102 Å °0.098 Å °-0.3501 Å °-0.0521 Å °0.1252 Å °
Refinement TLS groupSelection details: all

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