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Open data
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Basic information
Entry | Database: PDB / ID: 2w7d | ||||||
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Title | Crystal structure of Y51FbsSHMT internal aldimine | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rajaram, V. / Bhavani, B.S. / Bisht, S. / Kaul, P. / Prakash, V. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Importance of Tyrosine Residues of Bacillus Stearothermophilus Serine Hydroxymethyltransferase in Cofactor Binding and L-Allo-Thr Cleavage. Authors: Bhavani, B.S. / Rajaram, V. / Bisht, S. / Kaul, P. / Prakash, V. / Murthy, M.R.N. / Appaji Rao, N. / Savithri, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2w7eC ![]() 2w7fC ![]() 2w7gC ![]() 2w7hC ![]() 2w7iC ![]() 2w7jC ![]() 2w7kC ![]() 2w7lC ![]() 2w7mC ![]() 1kkjS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 44258.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF LINKAGE BETWEEN LYS A226 AND PLP A501 Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: Q7SIB6, ![]() | ||
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#2: Chemical | ChemComp-PLP / ![]() | ||
#3: Chemical | ChemComp-MPD / (![]() | ||
#4: Chemical | ChemComp-PO4 / ![]() | ||
#5: Water | ChemComp-HOH / ![]() | ||
Compound details | ENGINEEREDNonpolymer details | PYRIDOXAL 5' PHOSPHATE (PLP): A 501 COVALENTLY | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow![]() | Details: 50% MPD, 0.1M HEPES PH7.5, 0.2MM EDTA, 5 MM 2-MERCAPTOETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→30 Å / Num. obs: 35330 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KKJ Resolution: 1.8→23.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.427 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.19 Å
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Refine LS restraints |
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