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

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Basic information

Entry
Database: PDB / ID: 5yjl
TitleCrystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP
Components
  • Glutamyl-tRNA reductase 1
  • Glutamyl-tRNA reductase-binding protein
KeywordsPHOTOSYNTHESIS / GTR / ALA / tetrapyrrole
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 / chloroplast stroma ...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 / chloroplast stroma / heme biosynthetic process / protein-membrane adaptor activity / chloroplast / post-embryonic development / NADP binding / protein-containing complex
Similarity search - Function
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. ...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 / FMN-binding split barrel / Beta Polymerase; domain 2 / 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 / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glutamyl-tRNA reductase 1, chloroplastic / Glutamyl-tRNA reductase-binding protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhao, A. / Han, F.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31500243 China
CitationJournal: Photosyn. Res. / Year: 2018
Title: Crystal structure of Arabidopsis thaliana glutamyl-tRNAGlureductase in complex with NADPH and glutamyl-tRNAGlureductase binding protein
Authors: Zhao, A. / Han, F.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA reductase 1
C: Glutamyl-tRNA reductase-binding protein
B: Glutamyl-tRNA reductase 1
D: Glutamyl-tRNA reductase-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3126
Polymers172,8254
Non-polymers1,4872
Water5,909328
1
A: Glutamyl-tRNA reductase 1
B: Glutamyl-tRNA reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7674
Polymers104,2802
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-38 kcal/mol
Surface area37060 Å2
MethodPISA
2
C: Glutamyl-tRNA reductase-binding protein
D: Glutamyl-tRNA reductase-binding protein


Theoretical massNumber of molelcules
Total (without water)68,5452
Polymers68,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.340, 83.757, 344.581
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 Glutamyl-tRNA reductase 1 / / GluTR


Mass: 52139.902 Da / Num. of mol.: 2 / Fragment: UNP residues 73-543
Source method: isolated from a genetically manipulated source
Details: NAP / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HEMA1 / Plasmid: PMAL-C5X / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42804, glutamyl-tRNA reductase
#2: Protein Glutamyl-tRNA reductase-binding protein / 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: PGR7 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LU39
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 22.5%(w/v) PEG 3,350, 0.3M ammonium citrate tribasic, pH 7.0, 0.4mM NADPH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→32.958 Å / Num. obs: 48449 / % possible obs: 98.8 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 21.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.687 / Rsym value: 0.687 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7R

4n7r


Resolution: 2.7→32.958 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 2459 5.08 %
Rwork0.2134 --
obs0.2165 48449 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→32.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10153 0 96 328 10577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910461
X-RAY DIFFRACTIONf_angle_d1.11614189
X-RAY DIFFRACTIONf_dihedral_angle_d15.7683857
X-RAY DIFFRACTIONf_chiral_restr0.0421652
X-RAY DIFFRACTIONf_plane_restr0.0051814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75190.35881290.24912474X-RAY DIFFRACTION98
2.7519-2.8080.33081250.24562562X-RAY DIFFRACTION100
2.808-2.86910.35181260.24452564X-RAY DIFFRACTION98
2.8691-2.93580.34431280.24512498X-RAY DIFFRACTION99
2.9358-3.00910.31371340.23662536X-RAY DIFFRACTION98
3.0091-3.09040.27631330.22662503X-RAY DIFFRACTION99
3.0904-3.18130.30681390.22672531X-RAY DIFFRACTION98
3.1813-3.28390.31771330.21782538X-RAY DIFFRACTION100
3.2839-3.40120.29811440.22822519X-RAY DIFFRACTION98
3.4012-3.53720.29251400.21312552X-RAY DIFFRACTION99
3.5372-3.6980.26871380.20782549X-RAY DIFFRACTION99
3.698-3.89260.24781370.20262517X-RAY DIFFRACTION98
3.8926-4.13610.24641490.18992571X-RAY DIFFRACTION99
4.1361-4.45470.25381370.18632574X-RAY DIFFRACTION98
4.4547-4.90170.23551370.17692571X-RAY DIFFRACTION98
4.9017-5.6080.27231400.19622562X-RAY DIFFRACTION97
5.608-7.05410.28331450.24342626X-RAY DIFFRACTION99
7.0541-32.960.25161450.22752743X-RAY DIFFRACTION97

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