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- PDB-5che: Crystal structure of Arabidopsis glutamyl-tRNA reductase in compl... -

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Basic information

Entry
Database: PDB / ID: 5che
TitleCrystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its regulatory proteins
Components
  • Glutamyl-tRNA reductase 1, chloroplastic
  • Glutamyl-tRNA reductase-binding protein, chloroplastic
  • Protein FLUORESCENT IN BLUE LIGHT, chloroplastic
KeywordsOXIDOREDUCTASE / GluTR / tertiary complex / regulatory proteins / anchor protein
Function / homology
Function and homology information


glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / tetrapyrrole biosynthetic process / positive regulation of heme biosynthetic process / chloroplast membrane / chlorophyll biosynthetic process / chloroplast thylakoid / protoporphyrinogen IX biosynthetic process / photosynthetic electron transport chain / heme biosynthetic process ...glutamyl-tRNA reductase / glutamyl-tRNA reductase activity / tetrapyrrole biosynthetic process / positive regulation of heme biosynthetic process / chloroplast membrane / chlorophyll biosynthetic process / chloroplast thylakoid / protoporphyrinogen IX biosynthetic process / photosynthetic electron transport chain / heme biosynthetic process / chloroplast stroma / chloroplast thylakoid membrane / protein-membrane adaptor activity / post-embryonic development / chloroplast / NADP binding / protein-containing complex
Similarity search - Function
Protein FLUORESCENT IN BLUE LIGHT / Glutamyl-tRNA reductase, N-terminal domain / 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 ...Protein FLUORESCENT IN BLUE LIGHT / Glutamyl-tRNA reductase, N-terminal domain / 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. / PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Tetratricopeptide repeat / FMN-binding split barrel / Tetratricopeptide repeat domain / Beta Polymerase; domain 2 / TPR repeat region circular profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / NAD(P)-binding domain superfamily / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamyl-tRNA reductase 1, chloroplastic / Protein FLUORESCENT IN BLUE LIGHT, chloroplastic / Glutamyl-tRNA reductase-binding protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.203 Å
AuthorsFang, Y. / Liu, L.
CitationJournal: Sci Rep / Year: 2016
Title: The Arabidopsis glutamyl-tRNA reductase (GluTR) forms a ternary complex with FLU and GluTR-binding protein
Authors: Fang, Y. / Zhao, S. / Zhang, F. / Zhao, A. / Zhang, W. / Zhang, M. / Liu, L.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl-tRNA reductase 1, chloroplastic
B: Glutamyl-tRNA reductase 1, chloroplastic
C: Glutamyl-tRNA reductase-binding protein, chloroplastic
D: Glutamyl-tRNA reductase-binding protein, chloroplastic
E: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic
F: Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Theoretical massNumber of molelcules
Total (without water)208,3686
Polymers208,3686
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-62 kcal/mol
Surface area73360 Å2
Unit cell
Length a, b, c (Å)216.994, 53.211, 203.763
Angle α, β, γ (deg.)90.000, 108.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 52139.902 Da / Num. of mol.: 2 / Fragment: UNP residues 73-543
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 Glutamyl-tRNA reductase-binding protein, chloroplastic / GluTR-binding protein / Protein PROTON GRADIENT REGULATION 7


Mass: 34272.648 Da / Num. of mol.: 2 / Fragment: UNP residues 42-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLUTRBP, PGR7, At3g21200, MXL8.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LU39
#3: Protein Protein FLUORESCENT IN BLUE LIGHT, chloroplastic


Mass: 17771.264 Da / Num. of mol.: 2 / Fragment: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7 / Details: PEG 3350, sodium malonate, LiCl, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 36775 / Num. obs: 36775 / % possible obs: 99.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.68 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PHASERmodel building
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7R, 4YVQ

4n7r

4yvq


Resolution: 3.203→39.265 Å / FOM work R set: 0.7788 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1632 5.03 %
Rwork0.2227 30796 -
obs0.2255 32428 87.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.18 Å2 / Biso mean: 26.75 Å2 / Biso min: 1.43 Å2
Refinement stepCycle: final / Resolution: 3.203→39.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12342 0 0 6 12348
Biso mean---13.51 -
Num. residues----1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612561
X-RAY DIFFRACTIONf_angle_d0.97516948
X-RAY DIFFRACTIONf_chiral_restr0.0621941
X-RAY DIFFRACTIONf_plane_restr0.0042178
X-RAY DIFFRACTIONf_dihedral_angle_d10.724741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2028-3.2970.3798730.28981176124941
3.297-3.40340.34950.28541696179159
3.4034-3.5250.37011030.28362119222272
3.525-3.6660.2641100.25742433254383
3.666-3.83270.35691250.25552887301297
3.8327-4.03460.30731610.248228773038100
4.0346-4.28710.29411490.218729093058100
4.2871-4.61760.26271330.204329433076100
4.6176-5.08140.26871760.195429213097100
5.0814-5.81470.25551500.228829533103100
5.8147-7.31820.27711690.22592947311699
7.3182-39.26820.22041880.17332935312395

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