+Open data
-Basic information
Entry | Database: PDB / ID: 4k6n | ||||||
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Title | Crystal structure of yeast 4-amino-4-deoxychorismate lyase | ||||||
Components | Aminodeoxychorismate lyase | ||||||
Keywords | LYASE / PLP-dependent fold type IV enzyme / 4-amino-4-deoxychorismate / 4-aminobenzoate(PABA) / pyruvate / PLP | ||||||
Function / homology | Function and homology information aminodeoxychorismate lyase / 4-amino-4-deoxychorismate lyase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Dai, Y.-N. / Chi, C.-B. / Zhou, K. / Cheng, W. / Jiang, Y.-L. / Ren, Y.-M. / Chen, Y. / Zhou, C.-Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase Authors: Dai, Y.-N. / Chi, C.-B. / Zhou, K. / Cheng, W. / Jiang, Y.-L. / Ren, Y.-M. / Ruan, K. / Chen, Y. / Zhou, C.-Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k6n.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k6n.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k6n_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 4k6n_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 4k6n_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4k6n_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/4k6n ftp://data.pdbj.org/pub/pdb/validation_reports/k6/4k6n | 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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-Components
#1: Protein | Mass: 43837.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: ABZ2, YMR289W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q03266, aminodeoxychorismate lyase |
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#2: Chemical | ChemComp-PLP / |
#3: 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: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 20%(w/v) polyethylene glycol monomethyl ether 5000, 0.1M Bis-Tris, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97838 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97838 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 35258 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3478 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→36.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.786 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 98.38 Å2 / Biso mean: 31.658 Å2 / Biso min: 13.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.953 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -21.9982 Å / Origin y: 27.4282 Å / Origin z: -20.7569 Å
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