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Yorodumi- PDB-3emr: Crystal Structure Analysis of the ectoine hydroxylase ECTD from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3emr | ||||||
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Title | Crystal Structure Analysis of the ectoine hydroxylase ECTD from Salibacillus salexigens | ||||||
Components | EctD | ||||||
Keywords | OXIDOREDUCTASE / double stranded beta helix | ||||||
Function / homology | Function and homology information ectoine hydroxylase / ectoine catabolic process / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Virgibacillus salexigens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Reuter, K. / Heine, A. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD Authors: Reuter, K. / Pittelkow, M. / Bursy, J. / Heine, A. / Craan, T. / Bremer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3emr.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3emr.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3emr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3emr ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | ECTD HAS CLEARLY BEEN SHOWN BY SIZE EXCLUSION CHROMATOGRAPHY TO BE A MONOMER IN SOLUTION (BURSY ET AL. 2007, J. BIOL. CHEM. 282, PP31147-31155), AGAINST PISA'S SUGGESTION, A HOMODIMER. |
-Components
#1: Protein | Mass: 35980.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: cell / Source: (gene. exp.) Virgibacillus salexigens (bacteria) / Strain: DSM-11483 / Gene: ectD / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: Q2TDY4, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor | ||||
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#2: Chemical | ChemComp-FE / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.0M ammonium sulfate, 0.1M sodium fluoride, 2mM TCEP, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.85→50 Å / Num. all: 43040 / Num. obs: 43040 / % possible obs: 99.9 % / Redundancy: 14.6 % / Rsym value: 0.067 / Net I/σ(I): 34.1 | ||||||||||||||||||
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 2095 / Rsym value: 0.437 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→10 Å / Num. parameters: 9863 / Num. restraintsaints: 9313 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2071 / Occupancy sum non hydrogen: 2421.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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