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Yorodumi- PDB-3k1t: Crystal structure of Putative gamma-glutamylcysteine synthetase (... -
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-Basic information
Entry | Database: PDB / ID: 3k1t | ||||||
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Title | Crystal structure of Putative gamma-glutamylcysteine synthetase (YP_546622.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.90 A resolution | ||||||
Components | Glutamate--cysteine ligase GshA | ||||||
Keywords | LIGASE / Putative gamma-glutamylcysteine synthetase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Glutamate-cysteine ligase, N-terminal domain / Glutamate--cysteine ligase GshA / Glutamate--cysteine ligase GshA, N-terminal / Glutamate-cysteine ligase / ligase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Glutamate--cysteine ligase GshA Function and homology information | ||||||
Biological species | Methylobacillus flagellatus KT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative gamma-glutamylcysteine synthetase (YP_546622.1) from METHYLOBACILLUS FLAGELLATUS KT at 1.90 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 | 3k1t.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k1t.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 3k1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k1t_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3k1t_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 3k1t_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3k1t_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/3k1t ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k1t | HTTPS FTP |
-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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Unit cell |
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 48901.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria) Strain: KT / ATCC 51484 / DSM 6875 / Gene: Mfla_2516 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GYA6 | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.62 Å3/Da / Density % sol: 73.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.8000M ammonium sulfate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97882,0.91837 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→43.937 Å / Num. obs: 70491 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.665 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 18.11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→43.937 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.54 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.077 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROL (GOL),CHLORIDE (CL) AND SULFATE (SO4) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.15 Å2 / Biso mean: 21.64 Å2 / Biso min: 7.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.937 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 37.385 Å / Origin y: 80.5223 Å / Origin z: 20.716 Å
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