+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vmy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of F351GbsSHMT in complex with Gly and FTHF | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 163.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2vmnC ![]() 2vmoC ![]() 2vmpC ![]() 2vmqC ![]() 2vmrC ![]() 2vmsC ![]() 2vmtC ![]() 2vmuC ![]() 2vmvC ![]() 2vmwC ![]() 2vmxC ![]() 2vmzC ![]() 1kl2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 44184.062 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-405 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q7SIB6, ![]() |
---|
-Non-polymers , 5 types, 31 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/FFO.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/FFO.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | #5: Chemical | ChemComp-MRD / ( | ![]() #6: Water | ChemComp-HOH / | ![]() |
---|
-Details
Compound details | ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.96 % / Description: NONE |
---|---|
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 GLY, PROTEIN INCUBATED WITH 2 MM FTHF |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.7→30 Å / Num. obs: 19879 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 77.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KL2 Resolution: 2.7→20.81 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.029 / SU ML: 0.33 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 57.76 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|