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Yorodumi- PDB-2fzg: The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fzg | ||||||
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Title | The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.25 Resolution | ||||||
Components | (Aspartate carbamoyltransferase ...) x 2 | ||||||
Keywords | TRANSFERASE / Inhibitors / allosteric transition / Xray structures | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Heng, S. / Stieglitz, K.A. / Eldo, J. / Xia, J. / Cardia, J.P. / Kantrowitz, E.R. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: T-state Inhibitors of E. coli Aspartate Transcarbamoylase that Prevent the Allosteric Transition. Authors: Heng, S. / Stieglitz, K.A. / Eldo, J. / Xia, J. / Cardia, J.P. / Kantrowitz, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fzg.cif.gz | 206.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fzg.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 2fzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fzg_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2fzg_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2fzg_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 2fzg_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/2fzg ftp://data.pdbj.org/pub/pdb/validation_reports/fz/2fzg | HTTPS FTP |
-Related structure data
Related structure data | 2fzcC 2fzkC 1za2S 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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1 |
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Unit cell |
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-Components
-Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB / Plasmid: PEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17143.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI / Plasmid: PEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase |
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-Non-polymers , 4 types, 547 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 5.7 Details: ATCase holoenzyme was crystallized by microdialysis, using 50 L wells. The enzyme solution, at ~18 mg/mL, was dialyzed against a solution of 40 mM citric acid, 3 mM sodium azide, 1 mM 2- ...Details: ATCase holoenzyme was crystallized by microdialysis, using 50 L wells. The enzyme solution, at ~18 mg/mL, was dialyzed against a solution of 40 mM citric acid, 3 mM sodium azide, 1 mM 2-mercaptoethanol, 1 mM cytidine 5 -triphosphate, 0.2 mM EDTA (pH 5.7), MICRODIALYSIS, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.23 Å / Num. all: 79872 / Num. obs: 79872 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.62 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7836 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ZA2 Resolution: 2.25→28.23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→28.23 Å
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