+Open data
-Basic information
Entry | Database: PDB / ID: 4mhu | ||||||
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Title | Crystal structure of EctD from S. alaskensis with bound Fe | ||||||
Components | Ectoine hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / jelly-roll or cupin fold / ectoine hydroxylase / ectoine | ||||||
Function / homology | Function and homology information ectoine hydroxylase / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Sphingopyxis alaskensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Widderich, N. / Hoeppner, A. / Pittelkow, M. / Heider, J. / Smits, S.H. / Bremer, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal structure of the ectoine hydroxylase, a snapshot of the active site. Authors: Hoppner, A. / Widderich, N. / Lenders, M. / Bremer, E. / Smits, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mhu.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhu.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhu ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35226.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingopyxis alaskensis (bacteria) / Strain: DSM 13593 / LMG 18877 / RB2256 / Gene: Sala_2952 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW5 #2: Chemical | #3: Chemical | ChemComp-D9G / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES (pH 6.0), 200 mM Ca-acetate, 15-30 % (w/v) PEG 400 and 1.5-3.5 mM n-dodecyl-N N-dimethylglycine, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→46 Å / Num. all: 21776 / Num. obs: 20668 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.56→2.63 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.024 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.32 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.716 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→46 Å
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Refine LS restraints |
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