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Yorodumi- PDB-4iz6: Structure of EntE and EntB, an NRPS adenylation-PCP fusion protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iz6 | ||||||
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Title | Structure of EntE and EntB, an NRPS adenylation-PCP fusion protein with pseudo translational symmetry | ||||||
Components | Enterobactin synthase component E, Isochorismatase | ||||||
Keywords | LIGASE / Pseudo-translational symmetry / Adenylate-forming enzymes / ANL Superfamily / Non-ribosomal peptide synthetase / acyl carrier protein / NRPS adenylation domains and acyl carrier protein domain / 4'phosphopantetheinylation cofactor 4'PP / Chimera protein / fusion protein | ||||||
Function / homology | Function and homology information 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / isochorismatase / enterobactin synthase / isochorismatase activity / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / acyltransferase activity / phosphopantetheine binding ...2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / isochorismatase / enterobactin synthase / isochorismatase activity / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / acyltransferase activity / phosphopantetheine binding / magnesium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gulick, A.M. / Sundlov, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry. Authors: Sundlov, J.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 | 4iz6.cif.gz | 248 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iz6.ent.gz | 194.5 KB | Display | PDB format |
PDBx/mmJSON format | 4iz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iz6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4iz6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4iz6_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 4iz6_validation.cif.gz | 62.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/4iz6 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/4iz6 | HTTPS FTP |
-Related structure data
Related structure data | 3rg2S 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: 70408.641 Da / Num. of mol.: 2 / Fragment: Fusion between EntE(1-536) and EntB(211-285) Source method: isolated from a genetically manipulated source Details: insert contains a fusion between the entE gene, a 12 bp linker encoding Gly-Arg -Ala-Ser, and the fragment of the entB gene encoding residues 211 through 285. Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 Gene: b0594, entE, entE and entB, JW0586, b0595, entB, entG, JW0587 Plasmid: pSP55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P10378, UniProt: P0ADI4, (2,3-dihydroxybenzoyl)adenylate synthase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE 1HZ LIGAND IS ATTACHED TO PHOSPHOPANTETHEINE (PNS) THIOL (S44) TO FORM A COVALENT LINKAGE. THE ...THE 1HZ LIGAND IS ATTACHED TO PHOSPHOPAN | Sequence details | THE STRUCTURE IS A CHIMERIC PROTEIN OF ENTEROBACTIN SYNTHETASE COMPONENT E (ENTE) AND THE CARRIER ...THE STRUCTURE IS A CHIMERIC PROTEIN OF ENTEROBACT | |
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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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: The EntE-B protein crystallized via a modified vapor diffusion setup. A mother liquor of 20 % monomethyl ether PEG 2000 and 0.1 M bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS- ...Details: The EntE-B protein crystallized via a modified vapor diffusion setup. A mother liquor of 20 % monomethyl ether PEG 2000 and 0.1 M bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-TRIS) was made. The mother liquor was diluted 1:1 with the protein buffer for the crystallization reservoir and diluted 1:1 with protein solution for the hanging drop., pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2010 |
Radiation | Monochromator: SSRL 11-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→76.5 Å / Num. all: 52307 / Num. obs: 51261 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6837 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RG2 chain C residues 2-536 Resolution: 2.4→48.497 Å / SU ML: 0.88 / σ(F): 1.36 / Phase error: 37.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.376 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→48.497 Å
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Refine LS restraints |
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LS refinement shell |
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