+Open data
-Basic information
Entry | Database: PDB / ID: 6kvc | ||||||
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Title | MoeE5 in complex with UDP-glucose and NAD | ||||||
Components | MoeE5 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / substrate / complex / antibiotic / epimerase / galacturonic acid | ||||||
Function / homology | Function and homology information UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptomyces viridosporus ATCC 14672 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Ko, T.-P. / Liu, W. / Sun, H. / Liu, W. / Chen, C.-C. / Guo, R.-T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate. Authors: Sun, H. / Ko, T.P. / Liu, W. / Liu, W. / Zheng, Y. / Chen, C.C. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kvc.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kvc.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kvc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6kvc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6kvc_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 6kvc_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/6kvc ftp://data.pdbj.org/pub/pdb/validation_reports/kv/6kvc | HTTPS FTP |
-Related structure data
Related structure data | 6kv9C 4zrnS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36544.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces viridosporus ATCC 14672 (bacteria) Gene: moeE5 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A003 |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-UPG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na-citrate, Bis-Tris propane, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→25 Å / Num. obs: 42601 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4165 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4ZRN Resolution: 1.66→24.75 Å / SU ML: 0.1382 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.5802
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→24.75 Å
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Refine LS restraints |
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LS refinement shell |
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