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Yorodumi- PDB-2x3j: CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3j | ||||||
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Title | CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH ATP AND N-CITRYL-ETHYLENEDIAMINE 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 Å | ||||||
Authors | Schmelz, S. / Challis, G.L. / Naismith, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural Basis for Acyl Acceptor Specificity in the Achromobactin Biosynthetic Enzyme Acsd. Authors: Schmelz, S. / Botting, C.H. / Song, L. / Kadi, N.F. / 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 | 2x3j.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3j.ent.gz | 206.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x3j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2x3j_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2x3j_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 2x3j_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3j ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3j | 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 581 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-X3J / ( | #6: 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: 55 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ...Details: FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ETHYLENEDIAMINE, 10 MM MGCL2, 15 MM ATP AND 15 MM CITRATE. THE SUPERNATANT WAS USED TO GROW N-CITRYL-ETHYLENEDIAMINE CO-COMPLEX CRYSTALS IN HANGING DROPS FROM EQUAL MIXTURES WITH 0.1 M HEPES PH 7.2, 17% PEG 8000, 7.5% (V/V) GLYCEROL AT 20C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Date: Nov 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 89038 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 74.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FFE Resolution: 2→92.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.961 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.162 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.189 Å2
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Refinement step | Cycle: LAST / Resolution: 2→92.85 Å
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