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Yorodumi- PDB-4mp3: Staphyloferrin B precursor biosynthetic enzyme selenomethionine-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mp3 | ||||||
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Title | Staphyloferrin B precursor biosynthetic enzyme selenomethionine-labeled SbnB | ||||||
Components | Putative ornithine cyclodeaminase | ||||||
Keywords | OXIDOREDUCTASE / siderophore / L-Dap synthesis / ACEGA dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / thyroid hormone metabolic process / siderophore biosynthetic process / thyroid hormone binding / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å | ||||||
Authors | Grigg, J.C. / Kobylarz, M.J. / Rai, D.K. / Murphy, M.E.P. | ||||||
Citation | Journal: Chem.Biol. / Year: 2014 Title: Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor. Authors: Kobylarz, M.J. / Grigg, J.C. / Takayama, S.J. / Rai, D.K. / Heinrichs, D.E. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mp3.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mp3.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mp3_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 4mp3_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 4mp3_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4mp3_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/4mp3 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/4mp3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38495.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: NEWMAN / Gene: sbnB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NYS7, UniProt: A0A0H3K9Y6*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-tris, 0.2 M LiSO4, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97649 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2009 |
Radiation | Monochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SAD / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97649 Å / Relative weight: 1 |
Reflection | Resolution: 2.106→38.73 Å / Num. obs: 19092 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 |
Reflection shell | Highest resolution: 2.11 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.11→38.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.726 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 2.107 / ESU R: 0.234 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.73 Å2 / Biso mean: 36.326 Å2 / Biso min: 18.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→38.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.107→2.162 Å / 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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