+Open data
-Basic information
Entry | Database: PDB / ID: 7yqp | ||||||
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Title | Xcc Nicotinamide Phosphoribosyltransferase | ||||||
Components | Pre-B cell enhancing factor related protein | ||||||
Keywords | TRANSFERASE / NAMPT in isolation | ||||||
Function / homology | Function and homology information nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 Å | ||||||
Authors | Xu, G.L. / Ming, Z.H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of Xanthomonas campestris pv. campestris Nicotinamide Phosphoribosyltransferase: insights into bacterial NAD+ biosynthesis from the salvage pathway Authors: Xu, G.L. / Ming, Z.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yqp.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yqp.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yqp_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 7yqp_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 7yqp_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 7yqp_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/7yqp ftp://data.pdbj.org/pub/pdb/validation_reports/yq/7yqp | HTTPS FTP |
-Related structure data
Related structure data | 7yqoSC 7yqqC 7yqrC 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: 53213.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Strain: 8004 / Gene: XC_0719 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2X5R2 |
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#2: 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: 2.92 Å3/Da / Density % sol: 57.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: ammonium tartrate, N,N-Bis(3-D-gluconamidopropyl) cholamide, N,N-Dimethyldecylamine-N-oxide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→100.62 Å / Num. obs: 25813 / % possible obs: 100 % / Redundancy: 14.05 % / CC1/2: 1 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.08→9.3 Å / Num. unique obs: 2831 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YQO Resolution: 2.088→54.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.07 / 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: 145.63 Å2 / Biso mean: 56.8716 Å2 / Biso min: 25.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.088→54.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 41.2073 Å / Origin y: -45.5019 Å / Origin z: 3.8366 Å
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Refinement TLS group |
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