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- PDB-4bhd: Methanococcus jannaschii serine hydroxymethyl-transferase, apo form -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bhd | ||||||
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Title | Methanococcus jannaschii serine hydroxymethyl-transferase, apo form | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process ...Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saccoccia, F. / Angelucci, F. / Ilari, A. | ||||||
![]() | ![]() Title: The Crystal Structure of Archaeal Serine Hydroxymethyltransferase Reveals Idiosyncratic Features Likely Required to Withstand High Temperatures. Authors: Angelucci, F. / Morea, V. / Angelaccio, S. / Saccoccia, F. / Contestabile, R. / Ilari, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332 KB | Display | ![]() |
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PDB format | ![]() | 274.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uqvC ![]() 1kl2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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Components
#1: Protein | Mass: 48020.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q58992, glycine hydroxymethyltransferase, L-allo-threonine aldolase #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.22 % / Description: NONE |
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Crystal grow | pH: 5 / Details: NAH2PO4/K2HPO4 1.8 M, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 25528 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.93 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.53 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KL2 Resolution: 2.83→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.865 / SU B: 40.373 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / 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: 85.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→50 Å
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Refine LS restraints |
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