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Open data
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Basic information
Entry | Database: PDB / ID: 2vmt | ||||||
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Title | Crystal structure of Y60AbsSHMT L-Ser external aldimine | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / PLP-DEPENDENT ENZYMES / Y60A / FOLATE BINDING / PYRIDOXAL PHOSPHATE / ONE-CARBON METABOLISM | ||||||
Function / homology | ![]() glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rajaram, V. / Pai, V.R. / Bisht, S. / Bhavani, B.S. / Appaji Rao, N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structural and Functional Studies of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role of Asn(341), Tyr(60) and Phe(351) in Tetrahydrofolate Binding. Authors: Pai, V.R. / Rajaram, V. / Bisht, S. / Bhavani, B.S. / Rao, N.A. / Murthy, M.R.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 | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.9 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vmnC ![]() 2vmoC ![]() 2vmpC ![]() 2vmqC ![]() 2vmrC ![]() 2vmsC ![]() 2vmuC ![]() 2vmvC ![]() 2vmwC ![]() 2vmxC ![]() 2vmyC ![]() 2vmzC ![]() 1kl1S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44182.086 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF LINKAGE BETWEEN PLP B 501 AND SER B 502 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7SIB6, glycine hydroxymethyltransferase |
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-Non-polymers , 5 types, 397 molecules ![](data/chem/img/SER.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SER / |
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#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-MPD / ( |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED |
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-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 | pH: 7.5 Details: 50% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SER |
-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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→30 Å / Num. obs: 39211 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8 / % possible all: 73.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KL1 Resolution: 1.72→23.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.835 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / 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: 14.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→23.2 Å
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Refine LS restraints |
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