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Yorodumi- PDB-6yra: Crystal structure of ATP-dependent caprolactamase from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yra | ||||||
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Title | Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii | ||||||
Components |
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Keywords | HYDROLASE / Caprolactam hydrolase / nylon 6 monomer / 6-aminocaproic acid / 5-oxoproline / phosphocaprolactam / carboxyphosphate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas jessenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å | ||||||
Authors | Rozeboom, H.J. / Janssen, D.B. | ||||||
Citation | Journal: Proteins / Year: 2021 Title: Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. Authors: Marjanovic, A. / Rozeboom, H.J. / de Vries, M.S. / Mayer, C. / Otzen, M. / Wijma, H.J. / Janssen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yra.cif.gz | 960.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yra.ent.gz | 797.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yra_validation.pdf.gz | 343.9 KB | Display | wwPDB validaton report |
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Full document | 6yra_full_validation.pdf.gz | 399.4 KB | Display | |
Data in XML | 6yra_validation.xml.gz | 90.8 KB | Display | |
Data in CIF | 6yra_validation.cif.gz | 120.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yra ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yra | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 62799.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas jessenii (bacteria) / Gene: CRX42_01180 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A2W0FH34 #2: Protein | Mass: 75420.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas jessenii (bacteria) / Gene: CRX42_01175 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A2W0EVE0 #3: Chemical | Has ligand of interest | N | |
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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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 7.5, and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2018 |
Radiation | Monochromator: HeliosMX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 4→48.84 Å / Num. obs: 24725 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.632 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 4→4.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.252 / Num. unique obs: 4389 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L9W, 5M45, 5SVB Resolution: 4→48.84 Å / SU ML: 0.89 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→48.84 Å
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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