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Yorodumi- PDB-7wmw: Crystal structure of methylenetetrahydrofolate reductase MSMEG_66... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wmw | ||||||
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Title | Crystal structure of methylenetetrahydrofolate reductase MSMEG_6649 from Mycobacterium smegmatis | ||||||
Components | Methylenetetrahydrofolate reductase | ||||||
Keywords | TRANSFERASE / methylenetetrahydrofolate reductase | ||||||
Function / homology | : / Mycobacterial methylenetetrahydrofolate reductase / nucleotide binding / Methylenetetrahydrofolate reductase Function and homology information | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.053 Å | ||||||
Authors | Lin, W. / Wang, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.J. / Year: 2023 Title: Structural and functional characterization of a mycobacterial methylenetetrahydrofolate reductase utilizing NADH as the exclusive cofactor. Authors: Li, J. / Yang, M. / Li, W. / Lu, C. / Feng, D. / Shang, Z. / Wang, C. / Lin, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wmw.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wmw.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wmw_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 7wmw_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 7wmw_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7wmw_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wmw ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wmw | HTTPS FTP |
-Related structure data
Related structure data | 7wmxC 7wmyC 7wmzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32978.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6649 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R6S0 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Bis-Tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 36223 / % possible obs: 99.79 % / Redundancy: 16 % / CC1/2: 0.972 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.47 |
Reflection shell | Resolution: 2.05→2.07 Å / Num. unique obs: 36223 / CC1/2: 0.871 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.053→32.601 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.96 Å2 / Biso mean: 56.4975 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.053→32.601 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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