+Open data
-Basic information
Entry | Database: PDB / ID: 2i8u | ||||||
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Title | GDP-mannose mannosyl hydrolase-calcium-GDP product complex | ||||||
Components | GDP-mannose mannosyl hydrolase | ||||||
Keywords | HYDROLASE / Nudix enzyme / lipopolysaccharide | ||||||
Function / homology | Function and homology information GDP-mannose mannosyl hydrolase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Zou, Y. / Li, C. / Brunzelle, J.S. / Nair, S.K. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Molecular basis for substrate selectivity and specificity by an LPS biosynthetic enzyme Authors: Zou, Y. / Li, C. / Brunzelle, J.S. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i8u.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i8u.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 2i8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i8u_validation.pdf.gz | 498.8 KB | Display | wwPDB validaton report |
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Full document | 2i8u_full_validation.pdf.gz | 499.6 KB | Display | |
Data in XML | 2i8u_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 2i8u_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/2i8u ftp://data.pdbj.org/pub/pdb/validation_reports/i8/2i8u | HTTPS FTP |
-Related structure data
Related structure data | 2i8tC 2i8o 2i8p 2i8q 2i8r 2i8s 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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Unit cell |
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Details | Biological assembly is a dimer which is present as an NCS unit in the crystallographic asymmetric unit |
-Components
#1: Protein | Mass: 19344.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O128 / Gene: gmm / Plasmid: pET-14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6XQ58 #2: Chemical | #3: Chemical | #4: 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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10-20% PEG 4000 200 mM sodium acetate 100 mM HEPES, pH 8.0 harvested 72 hours after growth, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 77746 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.041 / Χ2: 1.05 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Num. unique all: 7466 / Χ2: 0.918 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.249 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→38.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.435 Å / Total num. of bins used: 20
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