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Yorodumi- PDB-1lua: Structure of methylene-tetrahydromethanopterin dehydrogenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lua | ||||||
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Title | Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1 complexed with NADP | ||||||
Components | Methylene Tetrahydromethanopterin Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta twisted open sheet structure | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / methylenetetrahydrofolate dehydrogenase (NADP+) / methylenetetrahydrofolate dehydrogenase (NADP+) activity / formaldehyde catabolic process / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ermler, U. / Hagemeier, C.H. / Roth, A. / Demmer, U. / Grabarse, W. / Warkentin, E. / Vorholt, J.A. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1. Authors: Ermler, U. / Hagemeier, C.H. / Roth, A. / Demmer, U. / Grabarse, W. / Warkentin, E. / Vorholt, J.A. #1: Journal: J.BACTERIOL. / Year: 1998 Title: The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1 Authors: Vorholt, J.A. / Chistoserdova, L. / Lidstrom, M.E. / Thauer, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lua.cif.gz | 184.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lua.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lua ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lua | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29640.609 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: mtdA / Plasmid: pET 17b CH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS References: UniProt: P55818, methylenetetrahydrofolate dehydrogenase (NADP+) #2: Chemical | #3: 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: 2.63 Å3/Da / Density % sol: 53.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 82475 / Num. obs: 82475 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / Num. unique all: 9753 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Methylene Tetrahydromethanopterin Dehydrogenase Resolution: 1.9→29.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 931083.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.4155 Å2 / ksol: 0.324197 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.263 / Rfactor Rwork: 0.213 |