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Yorodumi- PDB-2zsm: Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zsm | ||||||
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Title | Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix, hexagonal form | ||||||
Components | Glutamate-1-semialdehyde 2,1-aminomutase | ||||||
Keywords | ISOMERASE / PLP dependent enzyme / GSA / Cytoplasm / Porphyrin biosynthesis / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / protoporphyrinogen IX biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zsm.cif.gz | 260.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zsm.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zsm_validation.pdf.gz | 467.7 KB | Display | wwPDB validaton report |
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Full document | 2zsm_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 2zsm_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 2zsm_validation.cif.gz | 75.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/2zsm ftp://data.pdbj.org/pub/pdb/validation_reports/zs/2zsm | HTTPS FTP |
-Related structure data
Related structure data | 2epjC 2zslSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 46529.410 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q9Y9I9, glutamate-1-semialdehyde 2,1-aminomutase #2: Chemical | #3: Chemical | #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: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.5 Details: 0.8M NaH2PO4, 0.8M KH2PO4, 0.1M HEPES pH7.5, pH 4.5, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 6, 2007 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 71307 / Num. obs: 71307 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.6 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.133 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 6.79 / Num. unique all: 6219 / Rsym value: 0.365 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZSL Resolution: 2.3→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 6605563.67 / 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: 31.7561 Å2 / ksol: 0.349622 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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