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Yorodumi- PDB-7tm8: Crystal structure of Bifunctional adenosylcobalamin biosynthesis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tm8 | ||||||
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Title | Crystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae | ||||||
Components | Bifunctional adenosylcobalamin biosynthesis protein | ||||||
Keywords | TRANSFERASE / Bifunctional adenosylcobalamin biosynthesis protein / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | ||||||
Function / homology | Function and homology information adenosylcobinamide kinase / : / : / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tm8.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tm8.ent.gz | 168 KB | Display | PDB format |
PDBx/mmJSON format | 7tm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tm8_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 7tm8_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 7tm8_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 7tm8_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tm8 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tm8 | HTTPS FTP |
-Related structure data
Related structure data | 1c9kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20795.762 Da / Num. of mol.: 3 / Fragment: KlpnC.20504.a.B1 / Mutation: A75E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) Strain: HS11286 / Gene: KPHS_42470 / Plasmid: KlpnC.20504.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3GSH0, adenosylcobinamide kinase, adenosylcobinamide-phosphate guanylyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.62 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Index A4: 2.0 M Ammonium sulfate, 0.1 M BIS-TRIS, KlpnC.20504.a.B1.PW39083 at 40 mg/mL, Tray: plate 12369 well A4 drop 1, Puck: PSL0616, Cryo: 80% crystallant + 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.984 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→65.8 Å / Num. obs: 64185 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.034 / Rrim(I) all: 0.083 / Net I/σ(I): 12.4 / Num. measured all: 381328 / Scaling rejects: 8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C9K Resolution: 1.65→45.56 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.1 / 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: 73.55 Å2 / Biso mean: 25.8344 Å2 / Biso min: 12.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→45.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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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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