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Yorodumi- PDB-3c3d: Crystal structure of 2-phospho-(S)-lactate transferase from Metha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c3d | ||||||
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Title | Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46 | ||||||
Components | 2-phospho-L-lactate transferase | ||||||
Keywords | TRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Magnesium | ||||||
Function / homology | Function and homology information 2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / F420-0 metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Methanosarcina mazei Go1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. ...Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A.P. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Molecular insights into the biosynthesis of the f420 coenzyme. Authors: Forouhar, F. / Abashidze, M. / Xu, H. / Grochowski, L.L. / Seetharaman, J. / Hussain, M. / Kuzin, A. / Chen, Y. / Zhou, W. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Galinier, A. / White, R.H. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c3d.cif.gz | 250.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3d.ent.gz | 212.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c3d_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3c3d_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3c3d_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 3c3d_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3d ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34838.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Species: Methanosarcina mazei / Strain: Go1 / DSM 3647 / Goe1 / JCM 11883 / OCM 88 / Gene: cofD, MM_1874 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic References: UniProt: Q8PVT6, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-FO1 / #4: 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: 4.82 Å3/Da / Density % sol: 74.48 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM Lactyl phosphate, 5 mM DTT. Reservoir solution: 4.2 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2005 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.59 Å / Num. all: 178601 / Num. obs: 178601 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.084 / Net I/σ(I): 15.37 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.15 / Rsym value: 0.43 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→29.59 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 479729.46 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. Program XtalView has also been used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.7143 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
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