+Open data
-Basic information
Entry | Database: PDB / ID: 2hxb | ||||||
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Title | dCTP deaminase-dUTPase from Methanocaldococcus jannaschii | ||||||
Components | dCTP deaminase, dUMP-forming | ||||||
Keywords | HYDROLASE / beta barrel | ||||||
Function / homology | Function and homology information dCTP deaminase (dUMP-forming) / dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Bynck, J.H. / Johansson, E. | ||||||
Citation | Journal: To be Published Title: Structural evidence for a concerted Bifunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii Authors: Bynck, J.H. / Willemoes, M. / Larsen, S. / Johansson, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hxb.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hxb.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hxb_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 2hxb_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 2hxb_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 2hxb_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hxb ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hxb | HTTPS FTP |
-Related structure data
Related structure data | 2hxdC 1oghS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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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-Components
#1: Protein | Mass: 23461.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: dcd / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57872, dCTP deaminase (dUMP-forming) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30 % PEG400, 0.2M calcium chloride dihydrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 21, 2003 |
Radiation | Monochromator: Monochromator 0.900 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 14069 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.0127 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.55→2.61 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 4.8 / Num. unique all: 14069 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OGH Resolution: 2.55→25 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.096 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.183 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.602 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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