+Open data
-Basic information
Entry | Database: PDB / ID: 1rvu | ||||||
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Title | E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Components | Serine hydroxymethyltransferase, cytosolic | ||||||
Keywords | HYDROLASE / ONE CARBON METABOLISM | ||||||
Function / homology | Function and homology information cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate metabolic process ...cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Szebenyi, D.M. / Musayev, F.N. / Di Salvo, M.L. / Safo, M.K. / Schirch, V. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism. Authors: Szebenyi, D.M. / Musayev, F.N. / Di Salvo, M.L. / Safo, M.K. / Schirch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rvu.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rvu.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rvu ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rvu | HTTPS FTP |
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-Related structure data
Related structure data | 1rv3C 1rv4C 1rvyC 1cj0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains a homodimer. The biological assembly is a tetramer consisting of a pair of dimers. The second dimer in the tetramer is generate by the operation: y,x,1-z. |
-Components
#1: Protein | Mass: 52915.129 Da / Num. of mol.: 2 / Mutation: E75Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SHMT1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) References: UniProt: P07511, glycine hydroxymethyltransferase #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 4000, KCl, KMES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 27, 2003 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→57.3 Å / Num. all: 36699 / Num. obs: 36699 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.111 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 5219 / Rsym value: 0.544 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CJ0 Resolution: 2.5→57.33 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2600655.23 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.9808 Å2 / ksol: 0.339073 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→57.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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