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Yorodumi- PDB-3r6a: Crystal structure of an uncharacterized protein (hypothetical pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r6a | ||||||
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Title | Crystal structure of an uncharacterized protein (hypothetical protein MM_3218) from Methanosarcina mazei. | ||||||
Components | Uncharacterized protein | ||||||
Keywords | isomerase / lyase / PSI biology / Structural Genomics / New York Structural Genomics Research Consortium / Putative glyoxalase I / isomerase activity / NYSGRC | ||||||
Function / homology | lactoylglutathione lyase / lactoylglutathione lyase activity / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / ACETATE ION / Conserved protein Function and homology information | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein (hypothetical protein MM_3218) from Methanosarcina mazei. Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r6a.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r6a.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 3r6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/3r6a ftp://data.pdbj.org/pub/pdb/validation_reports/r6/3r6a | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | dimer |
-Components
#1: Protein | Mass: 16765.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: Glo_EDI_BRP_like, MM_3218 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8PS64, lactoylglutathione lyase #2: Chemical | ChemComp-ACT / | #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: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.1M ammonium sulfate; 0.1M Na acetate; Trehalose dihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→49.88 Å / Num. all: 32561 / Num. obs: 32561 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.76→1.81 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.588 / Num. unique all: 2536 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→43.82 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.76→43.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.87 Å / Rfactor Rfree error: 0.017
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