+Open data
-Basic information
Entry | Database: PDB / ID: 1upb | ||||||
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Title | Carboxyethylarginine synthase from Streptomyces clavuligerus | ||||||
Components | CARBOXYETHYLARGININE SYNTHASE | ||||||
Keywords | SYNTHASE / CLAVULANIC ACID / ANTIBIOTIC / LACTAMASE / FLAVOPROTEIN THIAMINE PYROPHOSPHATE | ||||||
Function / homology | Function and homology information N2-(2-carboxyethyl)arginine synthase / N2-(2-carboxyethyl)arginine synthase activity / acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Caines, M.E.C. / Elkins, J.M. / Hewitson, K.S. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure and Mechanistic Implications of N2-(2-Carboxyethyl)Arginine Synthase, the First Enzyme in the Clavulanic Acid Biosynthesis Pathway Authors: Caines, M.E.C. / Elkins, J.M. / Hewitson, K.S. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1upb.cif.gz | 429.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upb.ent.gz | 350.3 KB | Display | PDB format |
PDBx/mmJSON format | 1upb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1upb_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1upb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1upb_validation.xml.gz | 83.1 KB | Display | |
Data in CIF | 1upb_validation.cif.gz | 117.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upb ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SO4 / End label comp-ID: SO4 / Refine code: 4 / Auth seq-ID: 12 - 603 / Label seq-ID: 12
NCS oper:
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-Components
#1: Protein | Mass: 60964.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET24A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCV9 #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.6 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.6M (NH4)2SO4, 0.1M HEPES PH7.4, 10 MG/ML PROTEIN WITH 3-FOLD EXCESS OF TDP., pH 7.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.35 Å / Num. obs: 114144 / % possible obs: 92.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.8 / % possible all: 63.7 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 38.35 Å / Redundancy: 3.7 % / Num. measured all: 420132 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 63.7 % / Redundancy: 2.1 % / Num. unique obs: 11387 / Num. measured obs: 23614 / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.045 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→39 Å
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Refine LS restraints |
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