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- PDB-6cd0: Crystal structure of Medicago truncatula serine hydroxymethyltran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cd0 | ||||||
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Title | Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form | ||||||
![]() | (Serine hydroxymethyltransferase) x 2 | ||||||
![]() | TRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer | ||||||
Function / homology | ![]() glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z. | ||||||
![]() | ![]() Title: Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization. Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 722.5 KB | Display | ![]() |
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PDB format | ![]() | 593.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6cczSC ![]() 6cd1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49816.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: G7ILW0, glycine hydroxymethyltransferase #2: Protein | | Mass: 49588.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: G7ILW0, glycine hydroxymethyltransferase #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 55% Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2017 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→90 Å / Num. obs: 203236 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.063 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.74→1.84 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 32184 / Rrim(I) all: 1.06 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CCZ Resolution: 1.74→83.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.824 / SU B: 5.587 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.125 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→83.94 Å
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Refine LS restraints |
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