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- PDB-8z9u: Crystal structure of the Methermicoccus shengliensis ZC-1 2-metho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8z9u | ||||||
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Title | Crystal structure of the Methermicoccus shengliensis ZC-1 2-methoxybenzoic acid methyltransferase (MtxA) | ||||||
![]() | Tetrahydromethanopterin S-methyltransferase subunit H | ||||||
![]() | TRANSFERASE / Homodimers / Methyltransferase | ||||||
Function / homology | Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / tetrahydromethanopterin S-methyltransferase / Dihydropteroate synthase-like / methyltransferase activity / one-carbon metabolic process / methylation / Tetrahydromethanopterin S-methyltransferase subunit H![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Q. / Wang, S.X. / Bai, L.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Methermicoccus shengliensis ZC-1 2-methoxybenzoic acid methyltransferase (MtxA) Authors: Yang, Q. / Wang, S.X. / Bai, L.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 97.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 37873.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The sequence of organism Methermicoccus shengliensis DSM 18856 is not available, replaced by A0A832VZ83 temporarily. Source: (gene. exp.) ![]() Gene: mtrH, HA299_01740 / Production host: ![]() References: UniProt: A0A832VZ83, tetrahydromethanopterin S-methyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5 42% % v/v Polyethylene glycol 200 pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50.51 Å / Num. obs: 67410 / % possible obs: 95.28 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.91→2.051 Å / Num. unique obs: 58060 / CC1/2: 0.779 / CC star: 0.998 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→39.01 Å
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Refine LS restraints |
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LS refinement shell |
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