+Open data
-Basic information
Entry | Database: PDB / ID: 3n6q | ||||||
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Title | Crystal structure of YghZ from E. coli | ||||||
Components | YghZ aldo-keto reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel | ||||||
Function / homology | Function and homology information methylglyoxal catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / DNA damage response Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zubieta, C. / Totir, M. / Echols, N. / May, A. / Alber, T. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization. Authors: Totir, M. / Echols, N. / Nanao, M. / Gee, C.L. / Moskaleva, A. / Gradia, S. / Iavarone, A.T. / Berger, J.M. / May, A.P. / Zubieta, C. / Alber, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n6q.cif.gz | 552.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n6q.ent.gz | 453.1 KB | Display | PDB format |
PDBx/mmJSON format | 3n6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n6q_validation.pdf.gz | 495.5 KB | Display | wwPDB validaton report |
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Full document | 3n6q_full_validation.pdf.gz | 514.2 KB | Display | |
Data in XML | 3n6q_validation.xml.gz | 112.8 KB | Display | |
Data in CIF | 3n6q_validation.cif.gz | 171.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/3n6q ftp://data.pdbj.org/pub/pdb/validation_reports/n6/3n6q | HTTPS FTP |
-Related structure data
Related structure data | 2xhyC 3nbuC 3sboC 2a79S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38876.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: DH5alpha / References: UniProt: Q46851 #2: Chemical | ChemComp-MG / #3: 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: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M MgFormate, 0.1M MES pH 6, 7.5% PEG 20,000, 4% 1,4 butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 193K, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2007 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→98 Å / Num. all: 294303 / Num. obs: 294303 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.2 / Num. unique all: 42267 / Rsym value: 0.568 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A79 Resolution: 1.8→94.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.462 / SU ML: 0.075 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 1.3 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.239 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→94.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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