+Open data
-Basic information
Entry | Database: PDB / ID: 1m32 | ||||||
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Title | Crystal Structure of 2-aminoethylphosphonate Transaminase | ||||||
Components | 2-aminoethylphosphonate-pyruvate aminotransferase | ||||||
Keywords | TRANSFERASE / PLP-dependent aminotransferase fold | ||||||
Function / homology | Function and homology information 2-aminoethylphosphonate-pyruvate transaminase / 2-aminoethylphosphonate-pyruvate transaminase activity / organic phosphonate catabolic process Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Chen, C.C.H. / Zhang, H. / Kim, A.D. / Howard, A. / Sheldrick, G.M. / Mariano-Dunnaway, D. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Degradation Pathway of the Phosphonate Ciliatine: Crystal Structure of 2-Aminoethylphosphonate Transaminase Authors: Chen, C.C.H. / Zhang, H. / Kim, A.D. / Howard, A. / Sheldrick, G.M. / Mariano-Dunnaway, D. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m32.cif.gz | 486.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m32.ent.gz | 410 KB | Display | PDB format |
PDBx/mmJSON format | 1m32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m32_validation.pdf.gz | 528.6 KB | Display | wwPDB validaton report |
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Full document | 1m32_full_validation.pdf.gz | 565.9 KB | Display | |
Data in XML | 1m32_validation.xml.gz | 112.5 KB | Display | |
Data in CIF | 1m32_validation.cif.gz | 168.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/1m32 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/1m32 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 40675.422 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3) References: UniProt: P96060, 2-aminoethylphosphonate-pyruvate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ammonium acetate, sodium citrate, mmPEG5K, PLP, phosphate, DTT, phosphonoacetaldehyde, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.15→19.92 Å / Num. all: 264452 / Num. obs: 264452 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.5 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.152 / % possible all: 83 | ||||||||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 496002 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 83 % / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 9.8 % / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.005 | ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.188 |