[English] 日本語
Yorodumi- PDB-6tgh: SHMT from Streptococcus thermophilus Tyr55Thr variant in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tgh | ||||||
---|---|---|---|---|---|---|---|
Title | SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex | ||||||
Components | Serine hydroxymethyltransferase | ||||||
Keywords | TRANSFERASE / Pyridoxal phosphate / X-ray crystallography / hydroxymethyltransferase / proton abstraction / tetrahydrofolate-independent | ||||||
Function / homology | Function and homology information serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I. | ||||||
Citation | Journal: To Be Published Title: Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus Authors: Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tgh.cif.gz | 326.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tgh.ent.gz | 265.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/6tgh ftp://data.pdbj.org/pub/pdb/validation_reports/tg/6tgh | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ti1C 6ti3C 6yrwC 4wxbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ACBD
#1: Protein | Mass: 44944.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: glyA, CDA68_00974, DID82_07515 / Production host: Escherichia coli (E. coli) References: UniProt: Q5MCK9, UniProt: Q5M0B4*PLUS, glycine hydroxymethyltransferase |
---|
-Non-polymers , 5 types, 390 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.81 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: PLP 0.1 mm D-Serine 100 mm cacodylate 0.1 M, pH 6.5 sodium citrate 0.85 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→98 Å / Num. obs: 165927 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.2→2.2 Å / Rmerge(I) obs: 0.05 / Num. unique obs: 157619 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WXB Resolution: 2.12→47.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.021 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.82 Å2 / Biso mean: 55.166 Å2 / Biso min: 26.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.12→47.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.12→2.173 Å / Rfactor Rfree error: 0
|