+Open data
-Basic information
Entry | Database: PDB / ID: 7plb | |||||||||||||||
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Title | Caulobacter crescentus xylonolactonase with D-xylose | |||||||||||||||
Components | Smp-30/Cgr1 family protein | |||||||||||||||
Keywords | HYDROLASE / XylC / lactonase / mononuclear iron | |||||||||||||||
Function / homology | Function and homology information xylono-1,5-lactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / calcium ion binding Similarity search - Function | |||||||||||||||
Biological species | Caulobacter vibrioides (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | |||||||||||||||
Authors | Paakkonen, J. / Hakulinen, N. / Rouvinen, J. | |||||||||||||||
Funding support | Finland, 4items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed beta-propeller hydrolase family. Authors: Paakkonen, J. / Hakulinen, N. / Andberg, M. / Koivula, A. / Rouvinen, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7plb.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7plb.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 7plb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7plb_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7plb_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7plb_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 7plb_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/7plb ftp://data.pdbj.org/pub/pdb/validation_reports/pl/7plb | HTTPS FTP |
-Related structure data
Related structure data | 7plcC 7pldC 4gn7S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31687.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria) Strain: ATCC 19089 / CB15 / Gene: CC_0820 / Plasmid: pBAT4-XylC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A9Z1, EC: 3.1.1.68 |
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-Sugars , 2 types, 7 molecules
#4: Sugar | ChemComp-XYP / #5: Sugar | ChemComp-XYS / | |
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-Non-polymers , 3 types, 556 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.22 Å3/Da / Density % sol: 44.7 % / Description: Two-dimensional, rectangular |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, HEPES buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→85.58 Å / Num. obs: 61016 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6025 / CC1/2: 0.564 / Rpim(I) all: 0.719 / Rrim(I) all: 1.017 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GN7 Resolution: 1.73→85.47 Å / SU ML: 0.2463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2416 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→85.47 Å
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Refine LS restraints |
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LS refinement shell |
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