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Yorodumi- PDB-4cbs: X-ray structure of quintuple mutant of human alanine glyoxylate a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbs | ||||||
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Title | X-ray structure of quintuple mutant of human alanine glyoxylate aminotransferase, AGXT_RHEAM | ||||||
Components | SERINE--PYRUVATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / PRIMARY HIPEROXALURIA TYPE I / PROTEIN STABILIZATION | ||||||
Function / homology | Function and homology information oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process / glyoxylate catabolic process / Glyoxylate metabolism and glycine degradation / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / : / pyridoxal phosphate binding / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yunta, C. / Albert, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: The Consensus-Based Approach for Gene/Enzyme Replacement Therapies and Crystallization Strategies: The Case of Human Alanine:Glyoxylate Aminotransferase. Authors: Mesa-Torres, N. / Yunta, C. / Fabelo-Rosa, I. / Gonzalez-Rubio, J.M. / Sanchez-Ruiz, J.M. / Salido, E. / Albert, A. / Pey, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cbs.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbs.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbs ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbs | HTTPS FTP |
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-Related structure data
Related structure data | 4cbrC 2yobS 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: 43146.984 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS References: UniProt: P21549, alanine-glyoxylate transaminase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): SCHIFF BASE WITH K209 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.07 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 15% PEG 10K; 0.1 M HEPES PH 7.5, 2.5% V/V ISOPROPANOL AND 5% GLYCEROL AS ADDITIVE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→55.74 Å / Num. obs: 26518 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 8.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YOB Resolution: 2.3→55.741 Å / SU ML: 0.63 / σ(F): 1.5 / Phase error: 27.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.089 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→55.741 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.966 Å / Origin y: 12.7945 Å / Origin z: -21.2275 Å
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Refinement TLS group | Selection details: ALL |