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Yorodumi- PDB-2x3k: CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3k | ||||||
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Title | CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH AMP AND SULFATE FROM PECTOBACTERIUM CHRYSANTHEMI | ||||||
Components | ACSD | ||||||
Keywords | LIGASE / ALCALIGIN BIOSYNTHESIS / ALCC / 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 | ERWINIA CHRYSANTHEMI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Schmelz, S. / Naismith, J.H. | ||||||
Citation | Journal: Ph D Thesis / Year: 2010 Title: Adenylate Forming Enzymes Involved in Nrps-Independent Siderophore Biosynthesis Authors: Schmelz, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3k.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3k.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x3k_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2x3k_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2x3k_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 2x3k_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3k ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3k | HTTPS FTP |
-Related structure data
Related structure data | 3ffeS 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: 70598.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q93AT8 #2: Chemical | #3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM CACODYLATE PH 6.5, 29 % (W/V) PEG 8000 AND 200 MM (NH4)2SO4 AND 10 MM AMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.7 Å / Num. obs: 46179 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.7 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FFE Resolution: 2.5→39.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.121 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.303 / 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: 48.315 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→39.66 Å
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Refine LS restraints |
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