+Open data
-Basic information
Entry | Database: PDB / ID: 4itg | ||||||
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Title | P113S mutant of E. coli Cystathionine beta-lyase MetC | ||||||
Components | Cystathionine beta-lyase MetC | ||||||
Keywords | LYASE / Cystathionine beta-lyase / PLP adduct (LLP residue at amino acid 210) | ||||||
Function / homology | Function and homology information L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / alanine racemase activity / L-cysteine desulfhydrase activity / methionine biosynthetic process / transsulfuration / pyridoxal phosphate binding ...L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / alanine racemase activity / L-cysteine desulfhydrase activity / methionine biosynthetic process / transsulfuration / pyridoxal phosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Squire, C.J. / Yosaatmadja, Y. / Soo, V.W.C. / Patrick, W.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. Authors: Soo, V.W. / Yosaatmadja, Y. / Squire, C.J. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4itg.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4itg.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 4itg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4itg ftp://data.pdbj.org/pub/pdb/validation_reports/it/4itg | HTTPS FTP |
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-Related structure data
Related structure data | 4itxC 4wr3C 4xbjC 1cl1S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43479.352 Da / Num. of mol.: 2 / Mutation: P113S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3008, JW2975, metC / Production host: Escherichia coli (E. coli) / References: UniProt: P06721, cystathionine beta-lyase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2011 / Details: osmic |
Radiation | Monochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→19.4 Å / Num. all: 71753 / Num. obs: 71753 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 14.8 % / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CL1 Resolution: 1.74→19.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.191 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.781 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→19.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.784 Å / Total num. of bins used: 20
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