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Yorodumi- PDB-1bw9: PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bw9 | ||||||
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Title | PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE | ||||||
Components | (PHENYLALANINE ...) x 2 | ||||||
Keywords | AMINO ACID DEHYDROGENASE / OXIDATIVE DEAMINATION MECHANISM | ||||||
Function / homology | Function and homology information phenylalanine dehydrogenase / phenylalanine dehydrogenase activity / L-phenylalanine biosynthetic process / L-phenylalanine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Vanhooke, J.L. / Thoden, J.B. / Brunhuber, N.M.W. / Blanchard, J.L. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism. Authors: Vanhooke, J.L. / Thoden, J.B. / Brunhuber, N.M. / Blanchard, J.S. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bw9.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bw9.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bw9 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bw9 | 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
-PHENYLALANINE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36559.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Cell line: BL21 / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q59771, phenylalanine dehydrogenase |
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#2: Protein | Mass: 36615.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Cell line: BL21 / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q59771, phenylalanine dehydrogenase |
-Non-polymers , 8 types, 1037 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Chemical | #9: Chemical | ChemComp-IPA / #10: 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: 2.9 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.7 / Details: pH 8.7 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding | |||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 1.03 |
Detector | Detector: CCD / Date: Feb 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 121716 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.23 / % possible all: 77 |
Reflection | *PLUS Num. measured all: 461544 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 77 % / Num. unique obs: 12631 / Rmerge(I) obs: 0.236 / Num. measured obs: 41195 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 433.9 Å2 / ksol: 1.064 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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