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- PDB-8ssj: Room-temperature X-ray structure of human mitochondrial serine hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ssj | ||||||
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Title | Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) | ||||||
![]() | Serine hydroxymethyltransferase, mitochondrial![]() | ||||||
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Function / homology | ![]() BRISC complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Drago, V.N. / Kovalevsky, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography. Authors: Drago, V.N. / Campos, C. / Hooper, M. / Collins, A. / Gerlits, O. / Weiss, K.L. / Blakeley, M.P. / Phillips, R.S. / Kovalevsky, 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 | ![]() | 198 KB | Display | ![]() |
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PDB format | ![]() | 154.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ssyC ![]() 8suiC ![]() 8sujC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 52143.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P34897, ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.14 % |
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Crystal grow![]() | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.1 M Tricine pH 8.4, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 55062 / % possible obs: 97 % / Redundancy: 6 % / CC1/2: 0.98 / Rpim(I) all: 0.063 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 5150 / CC1/2: 0.765 / Rpim(I) all: 0.291 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.65 Å
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Refine LS restraints |
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LS refinement shell |
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