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Yorodumi- PDB-1c1x: L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c1x | ||||||
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Title | L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND L-3-PHENYLLACTATE | ||||||
Components |
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Keywords | OXIDOREDUCTASE / 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 / Resolution: 1.4 Å | ||||||
Authors | Vanhooke, J.L. / Thoden, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity. Authors: Brunhuber, N.M. / Thoden, J.B. / Blanchard, J.S. / Vanhooke, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c1x.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c1x.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c1x_validation.pdf.gz | 575 KB | Display | wwPDB validaton report |
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Full document | 1c1x_full_validation.pdf.gz | 595.7 KB | Display | |
Data in XML | 1c1x_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1c1x_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1x ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36428.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Plasmid: PBL-1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59771 |
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#2: Protein | Mass: 36484.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / References: UniProt: Q59771 |
-Non-polymers , 7 types, 857 molecules
#3: Chemical | ChemComp-K / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Chemical | #9: 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: 2.77 Å3/Da / Density % sol: 55.63 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: macroseeded into batch / pH: 8.7 Details: 1.2 M NA/K PHOSPHATE 50 MM CHES 2% ISOPROPANOL 5 MM NAD+ 10 MM L-3- PHENYLLACTATE 3.75 MG/ML PROTEIN, pH 8.7, MACROSEEDED INTO BATCH, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7433 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7433 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 156183 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / % possible all: 94.7 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Num. measured all: 735380 / Biso Wilson estimate: 0 Å2 |
Reflection shell | *PLUS % possible obs: 94.7 % / Redundancy: 3.4 % / Num. unique obs: 15057 / Num. measured obs: 50914 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Resolution: 1.4→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor all: 0.183 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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