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Yorodumi- PDB-1c4x: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE (BPHD) FROM R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c4x | ||||||
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Title | 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE (BPHD) FROM RHODOCOCCUS SP. STRAIN RHA1 | ||||||
Components | PROTEIN (2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE) | ||||||
Keywords | HYDROLASE / PCB DEGRADATION | ||||||
Function / homology | Function and homology information 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | ||||||
Authors | Nandhagopal, N. / Senda, T. / Mitsui, Y. | ||||||
Citation | Journal: Proc.Jpn.Acad.,Ser.B / Year: 1997 Title: Three-Dimensional Structure of Microbial 2-Hydroxyl-6-Oxo-6-Phenylhexa-2,4- Dienoic Acid (Hpda) Hydrolase (Bphd Enzyme) from Rhodococcus Sp. Strain Rha1, in the Pcb Degradation Pathway Authors: Nandhagopal, N. / Senda, T. / Hatta, T. / Yamada, A. / Masai, E. / Fukuda, M. / Mitsui, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c4x.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c4x.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c4x ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c4x | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31680.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Production host: Escherichia coli (E. coli) References: UniProt: O05149, UniProt: Q75WN8*PLUS, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase |
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#2: 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: 3.26 Å3/Da / Density % sol: 62 % |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 15274 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→100 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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