+Open data
-Basic information
Entry | Database: PDB / ID: 1b74 | ||||||
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Title | GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS | ||||||
Components | GLUTAMATE RACEMASE | ||||||
Keywords | ISOMERASE / RACEMASE | ||||||
Function / homology | Function and homology information glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Aquifex pyrophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Hwang, K.Y. / Cho, C.S. / Kim, S.S. / Yu, Y.G. / Cho, Y. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure and mechanism of glutamate racemase from Aquifex pyrophilus. Authors: Hwang, K.Y. / Cho, C.S. / Kim, S.S. / Sung, H.C. / Yu, Y.G. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b74.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b74.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b74 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b74 | HTTPS FTP |
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-Related 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: 27978.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aquifex pyrophilus (bacteria) / References: UniProt: P56868, glutamate racemase |
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#2: Chemical | ChemComp-DGN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.000, 1.015, 1.1 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→8 Å / Num. obs: 11546 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.087 |
-Processing
Software | Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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