+Open data
-Basic information
Entry | Database: PDB / ID: 5xnz | |||||||||||||||
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Title | Crystal structure of CreD complex with fumarate | |||||||||||||||
Components | CreD | |||||||||||||||
Keywords | LYASE / fumarase / cremeomycin / nitrous acid | |||||||||||||||
Function / homology | Function and homology information nitrosuccinate lyase / 3-carboxy-cis,cis-muconate cycloisomerase activity / 3,4-dihydroxybenzoate catabolic process / lyase activity Similarity search - Function | |||||||||||||||
Biological species | Streptomyces cremeus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||||||||
Authors | Katsuyama, Y. / Sato, Y. / Sugai, Y. / Higashiyama, Y. / Senda, M. / Senda, T. / Ohnishi, Y. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: FEBS J. / Year: 2018 Title: Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination Authors: Katsuyama, Y. / Sato, Y. / Sugai, Y. / Higashiyama, Y. / Senda, M. / Senda, T. / Ohnishi, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xnz.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xnz.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xnz ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xnz | HTTPS FTP |
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-Related structure data
Related structure data | 5xnySC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 50804.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cremeus (bacteria) / Gene: creD / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0K2JL82 | ||
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#2: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.17 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1 M Tris-HCl, pH 8.2-8.5 containing 1.8-2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2016 | ||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.3→19.85 Å / Num. obs: 39878 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.97 % / Biso Wilson estimate: 35.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.085 / Χ2: 0.998 / Net I/σ(I): 17.08 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XNY Resolution: 2.3→19.85 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.12 / Stereochemistry target values: ML Details: The entry contains Friedel pairs in F_Plus/Minus columns.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.85 Å
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Refine LS restraints |
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LS refinement shell |
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