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Yorodumi- PDB-2x0q: CO-COMPLEX STRUCTURE OF ALCALIGIN BIOSYNTHESIS PROTEIN C (ALCC) W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x0q | ||||||
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Title | CO-COMPLEX STRUCTURE OF ALCALIGIN BIOSYNTHESIS PROTEIN C (ALCC) WITH ATP FROM Bordetella bronchiseptica | ||||||
Components | ALCALIGIN BIOSYNTHESIS PROTEIN | ||||||
Keywords | BIOSYNTHETIC PROTEIN / ALCALIGIN BIOSYNTHESIS / ADENYLATION / SIDEROPHORES / IRON ACQUISITION | ||||||
Function / homology | Function and homology information acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | BORDETELLA BRONCHISEPTICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Schmelz, S. / Challis, G.L. / Naismith, J.H. | ||||||
Citation | Journal: To be Published Title: Co-Complex Structure of Alcaligin Biosynthesis Protein C (Alcc) with ATP from Bordetella Bronchiseptica Authors: Schmelz, S. / Challis, G.L. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x0q.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x0q.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/2x0q ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x0q | HTTPS FTP |
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-Related structure data
Related structure data | 2x0oS S: Starting model for refinement |
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Similar 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: 70047.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Plasmid: PET-151/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94255, UniProt: Q7W557*PLUS | ||
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#2: Chemical | ChemComp-ATP / | ||
#3: Chemical | #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 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH 6.5, 1.7 M MGSO4, 0.18 M LI2S04 AND PROTEIN SOLUTION (2.5 MG/ML ALCC, 45 MM MES PH 6.5 AND 5 MM ADENOSINE, 5 MM N-HYDROXY-N-SUCCINYLPUTRESCINE, PRE INCUBATED FOR 30 MIN ON ICE), ...Details: 0.1 M MES PH 6.5, 1.7 M MGSO4, 0.18 M LI2S04 AND PROTEIN SOLUTION (2.5 MG/ML ALCC, 45 MM MES PH 6.5 AND 5 MM ADENOSINE, 5 MM N-HYDROXY-N-SUCCINYLPUTRESCINE, PRE INCUBATED FOR 30 MIN ON ICE), CRYSTALS SOAKED IN 25 MM ATP, 25 MM N-HYDROXY-N-SUCCINYLPUTRESCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 41914 / % possible obs: 99.9 % / Observed criterion σ(I): 3.5 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X0O Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.713 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / 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: 21.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→50 Å
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Refine LS restraints |
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