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- PDB-1eqb: X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1eqb | ||||||
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Title | X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / Functional mutant / hydroxymethyltransferase / aat-like fold / one carbon metabolism | ||||||
Function / homology | ![]() glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion ...glycine catabolic process / L-allo-threonine aldolase activity / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Contestabile, R. / Angelaccio, S. / Bossa, F. / Wright, H.T. / Scarsdale, N. / Kazanina, G. / Schirch, V. | ||||||
![]() | ![]() Title: Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase. Authors: Contestabile, R. / Angelaccio, S. / Bossa, F. / Wright, H.T. / Scarsdale, N. / Kazanina, G. / Schirch, V. #1: ![]() Title: Crystal Structure at 2.4 Angstrom Resolution of E. Coli Serine Hydroxymethyltransferase in Complex with Glycine Substrate and 5-Formyl Tetrahydrofolate Authors: Scarsdale, J.N. / Radaev, S. / Kazanina, G. / Schirch, V. / Wright, H.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.6 KB | Display | ![]() |
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PDB format | ![]() | 249 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 64.5 KB | Display | |
Data in CIF | ![]() | 85.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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2 | ![]()
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Unit cell |
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Details | Biological assembly is a dimer composed of two monomers. The assymetric unit contains two such dimers. One dimer consists of monomers A + B and the other consists of monomers C + D. |
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Components
#1: Protein | Mass: 45356.477 Da / Num. of mol.: 4 / Mutation: Y65F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00477, UniProt: P0A825*PLUS, glycine hydroxymethyltransferase #2: Chemical | ChemComp-GLY / #3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-FFO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.2 Details: 2M K3PO4, pH 7.2, VAPOR DIFFUSION, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→92 Å / Num. all: 66775 / Num. obs: 63328 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 5.53 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1 / Num. unique all: 2865 / % possible all: 86.1 |
Reflection shell | *PLUS % possible obs: 96.1 % / Mean I/σ(I) obs: 1.09 |
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Processing
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Refinement | Resolution: 2.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2118892.63 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.76 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.03 Å / Weight position: 150 | ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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