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Yorodumi- PDB-1j6r: Crystal structure of Activation (AdoMet binding) domain of Methio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j6r | ||||||
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Title | Crystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution | ||||||
Components | METHIONINE SYNTHASE | ||||||
Keywords | TRANSFERASE / STRUCTURAL GENOMICS / TM0269 / ACTIVATION (ADOMET BINDING) DOMAIN OF METHIONINE SYNTHASE / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | NADH Oxidase - #40 / S-adenosyl-L-methionine dependent methionine synthase, predicted / Vitamin B12-dependent methionine synthase, activation domain superfamily / methionine synthase activity / NADH Oxidase / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j6r.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j6r.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 1j6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j6r_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 1j6r_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 1j6r_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1j6r_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/1j6r ftp://data.pdbj.org/pub/pdb/validation_reports/j6/1j6r | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24383.975 Da / Num. of mol.: 2 / Fragment: ACTIVATION (ADOMET BINDING) DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYA6, methionine synthase #2: 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: 2.99 Å3/Da / Density % sol: 58.81 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 2.4 M Ammonium Sulfate; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.979029 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2001 | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→36.22 Å / Num. obs: 27922 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 43.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 14 | |||||||||
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.344 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→36.22 Å / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: ...Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: 179,180. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Solvent model: BULK SOLVENT MODELLING / Bsol: 322.79 Å2 / ksol: 0.9 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.59 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→36.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.41 Å / Total num. of bins used: 20
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