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Yorodumi- PDB-8pml: Structure of Nal1 protein , SPIKE allele from japonica rice, cons... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pml | |||||||||||||||
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Title | Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458 | |||||||||||||||
Components | Protein NARROW LEAF 1 | |||||||||||||||
Keywords | PLANT PROTEIN / Serine protease | |||||||||||||||
Function / homology | stem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / nucleoplasm / cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / Protein NARROW LEAF 1 Function and homology information | |||||||||||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||||||||
Authors | Huang, L.Y. / Rety, S. / Xi, X.G. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nat Plants / Year: 2024 Title: The catalytic triad of rice NARROW LEAF1 involves H234. Authors: Ling-Yun Huang / Na-Nv Liu / Wei-Fei Chen / Xia Ai / Hai-Hong Li / Ze-Lin Zhang / Xi-Miao Hou / Philippe Fossé / Olivier Mauffret / Dong-Sheng Lei / Stephane Rety / Xu-Guang Xi / Abstract: NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that ...NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pml.cif.gz | 984.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pml.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pml ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pml | HTTPS FTP |
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-Related structure data
Related structure data | 8pmeC 8pmgC 8pmiC 8pmmC 8pn1C 8pn2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45211.141 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147 Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4XT64 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES 10% PEG 5000 MME 10% 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97869 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2.948→129.924 Å / Num. obs: 47426 / % possible obs: 90.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 71.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.067 / Rrim(I) all: 0.245 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.948→3.19 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.957 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2372 / CC1/2: 0.644 / Rpim(I) all: 0.553 / Rrim(I) all: 2.035 / % possible all: 52.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→87.71 Å / SU ML: 0.3696 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.8077 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→87.71 Å
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Refine LS restraints |
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LS refinement shell |
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