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Yorodumi- PDB-2fq1: Crystal structure of the two-domain non-ribosomal peptide synthet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fq1 | ||||||
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Title | Crystal structure of the two-domain non-ribosomal peptide synthetase EntB containing isochorismate lyase and aryl-carrier protein domains | ||||||
Components | Isochorismatase | ||||||
Keywords | HYDROLASE / EntB / NRPS / multi-domain / ACP | ||||||
Function / homology | Function and homology information isochorismatase / enterobactin synthase / isochorismatase activity / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / phosphopantetheine binding / magnesium ion binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Drake, E.J. / Nicolai, D.A. / Gulick, A.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2006 Title: Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain. Authors: Drake, E.J. / Nicolai, D.A. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fq1.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fq1.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fq1_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 2fq1_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 2fq1_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2fq1_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/2fq1 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/2fq1 | HTTPS FTP |
-Related structure data
Related structure data | 1nf9S 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: 32787.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: entB, entG / Plasmid: pRF7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADI4, isochorismatase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-EDO / | #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: 2.65 Å3/Da / Density % sol: 53.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10-15% mePEG5000, 0.8M MgCl2, 10% ethylene glycol, 50mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 26, 2004 / Details: Osmic Max-Flux Confocal Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 31192 / Num. obs: 30038 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.304 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.341 / Num. unique all: 2423 / Χ2: 0.608 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1NF9 Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.037 / SU ML: 0.176 / SU R Cruickshank DPI: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.233 / Stereochemistry target values: Engh & Huber
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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 mean: 45.001 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.361 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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