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Yorodumi- PDB-4erg: Evidence for a Dual Role of an Active Site Histidine in alpha-Ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4erg | ||||||
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Title | Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase | ||||||
Components | 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase | ||||||
Keywords | LYASE / tim-barrel / decarboxylase / metal-binding / Fe | ||||||
Function / homology | Function and homology information organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 Å | ||||||
Authors | Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que Jr., L. / Liu, A. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase Authors: Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que, L. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4erg.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4erg.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 4erg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4erg ftp://data.pdbj.org/pub/pdb/validation_reports/er/4erg | HTTPS FTP |
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-Related structure data
Related structure data | 4epkC 4eraC 4eriC 2hbxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37208.621 Da / Num. of mol.: 2 / Mutation: H228Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): ESCHERICHIA COLI BL21(DE3) / References: UniProt: Q83V25 #2: Chemical | #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: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17% PEG 5000, 0.1M Tris, 0.2 M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.789→83.77 Å / Num. all: 18046 / Num. obs: 18010 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 60.8 |
Reflection shell | Resolution: 2.789→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.49 / Num. unique all: 879 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HBX Resolution: 2.789→83.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.915 / SU B: 19.436 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 86.192 Å2
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Refinement step | Cycle: LAST / Resolution: 2.789→83.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.789→2.862 Å / Total num. of bins used: 20
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