+Open data
-Basic information
Entry | Database: PDB / ID: 3000000000000 | ||||||
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Title | Cu2+ substituted Aquifex aeolicus KDO8PS in complex with KDO8P | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / KDO / KDO8PS / Copper / PEP / metal geometry / cytoplasm / Lipopolysaccharide biosynthesis | ||||||
Function / homology | Function and homology information monosaccharide biosynthetic process / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Gatti, D.L. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis. Authors: Kona, F. / Tao, P. / Martin, P. / Xu, X. / Gatti, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e12.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e12.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 3e12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e12_validation.pdf.gz | 954.6 KB | Display | wwPDB validaton report |
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Full document | 3e12_full_validation.pdf.gz | 967.8 KB | Display | |
Data in XML | 3e12_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3e12_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/3e12 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/3e12 | HTTPS FTP |
-Related structure data
Related structure data | 1fwsC 1fwwSC 2a21C 2a2iC 3e0iC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29774.406 Da / Num. of mol.: 2 / Fragment: KDO8PS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: kdsA, aq_085 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase |
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-Non-polymers , 5 types, 550 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 2.79 Å3/Da / Density % sol: 55.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: PEG 4000, NA ACETATE, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→22.3 Å / Num. all: 73917 / Num. obs: 73254 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 21.2 % / Biso Wilson estimate: 20.68 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1FWW Resolution: 1.7→22.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.567 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089 / 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: 21.589 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→22.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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