+Open data
-Basic information
Entry | Database: PDB / ID: 4p69 | ||||||
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Title | Acek (D477A) ICDH complex | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/OXIDOREDUCTASE / HYDROLASE-OXIDOREDUCTASE complex | ||||||
Function / homology | Function and homology information [isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / guanosine tetraphosphate binding / AMP binding / phosphoprotein phosphatase activity / tricarboxylic acid cycle ...[isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / guanosine tetraphosphate binding / AMP binding / phosphoprotein phosphatase activity / tricarboxylic acid cycle / electron transport chain / glucose metabolic process / NAD binding / response to oxidative stress / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å | ||||||
Authors | Jimin, Z. / Nan, W. / Shu, W. / Zongchao, J. | ||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2014 Title: The phosphatase mechanism of bifunctional kinase/phosphatase AceK. Authors: Wang, S. / Shen, Q. / Chen, G. / Zheng, J. / Tan, H. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p69.cif.gz | 404.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p69.ent.gz | 321.4 KB | Display | PDB format |
PDBx/mmJSON format | 4p69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p69_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4p69_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4p69_validation.xml.gz | 68.5 KB | Display | |
Data in CIF | 4p69_validation.cif.gz | 96.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p69 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p69 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 66495.984 Da / Num. of mol.: 2 / Fragment: residues 4-571 / Mutation: D477A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: aceK, Z5602, ECs4934 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3 References: UniProt: Q8X607, [isocitrate dehydrogenase (NADP+)] kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Protein | Mass: 45678.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: icd, icdA, icdE, b1136, JW1122 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3 References: UniProt: P08200, isocitrate dehydrogenase (NADP+) #3: Chemical | #4: Chemical | #5: 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: 3.95 Å3/Da / Density % sol: 68.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2mM DTT, 10% glycerol, 0.1M MES pH 6.0, 25%~30% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3.3→19.96 Å / Num. obs: 27331 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.044 / Net I/σ(I): 14.5 / Num. measured all: 367390 / Scaling rejects: 446 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 3.3→29.97 Å / WRfactor Rfree: 0.2338 / WRfactor Rwork: 0.1716 / FOM work R set: 0.8291 / SU B: 20.11 / SU ML: 0.337 / SU Rfree: 2.0802 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 2.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 193.58 Å2 / Biso mean: 81.787 Å2 / Biso min: 42.42 Å2
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Refinement step | Cycle: final / Resolution: 3.3→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.386 Å / Total num. of bins used: 20
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