+Open data
-Basic information
Entry | Database: PDB / ID: 7xps | ||||||
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Title | Crystal structrue of MtdL:GDP:Mn | ||||||
Components | Transglycosylse | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | STELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / GUANOSINE-5'-DIPHOSPHATE / : / Transglycosylse Function and homology information | ||||||
Biological species | Marinactinospora thermotolerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, F.D. / He, C. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn 2+ coordination and substrate binding. Authors: Du, X. / Chu, X. / Liu, N. / Jia, X. / Peng, H. / Xiao, Y. / Liu, L. / Yu, H. / Li, F. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xps.cif.gz | 317.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xps.ent.gz | 256.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xps_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7xps_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7xps_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 7xps_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/7xps ftp://data.pdbj.org/pub/pdb/validation_reports/xp/7xps | HTTPS FTP |
-Related structure data
Related structure data | 7xprSC 7xptC 7xpuC 7xpvC 8hl8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 41791.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinactinospora thermotolerans (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: G8HX37 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate, pH 5.6, 15% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→19.85 Å / Num. obs: 54465 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Rrim(I) all: 0.14 / Net I/σ(I): 15.2 / Num. measured all: 723926 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XPR Resolution: 2.1→19.85 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.89 / Stereochemistry target values: ML
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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 max: 114.69 Å2 / Biso mean: 33.051 Å2 / Biso min: 15.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→19.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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