+Open data
-Basic information
Entry | Database: PDB / ID: 1nbe | ||||||
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Title | ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN MUTANT (T82A) | ||||||
Components | (ASPARTATE TRANSCARBAMOYLASE) x 2 | ||||||
Keywords | TRANSFERASE / ATCASE / ALLOSTERY / PYRIMIDINE BIOSYNTHESIS | ||||||
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 / RIGID BODY / Resolution: 2.6 Å | ||||||
Authors | Williams, M.K. / Stec, B. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: A single mutation in the regulatory chain of Escherichia coli aspartate transcarbamoylase results in an extreme T-state structure. Authors: Williams, M.K. / Stec, B. / Kantrowitz, E.R. #1: Journal: Biochemistry / Year: 1990 Title: Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP-and Ctp-Complexed Enzymes at 2.6-A Resolution Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N. #2: Journal: Biochemistry / Year: 1990 Title: Erratum. Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP-and Ctp-Complexed Enzymes at 2.6-A Resolution Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbe.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbe.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbe_validation.pdf.gz | 409 KB | Display | wwPDB validaton report |
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Full document | 1nbe_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 1nbe_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 1nbe_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbe ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbe | HTTPS FTP |
-Related structure data
Related structure data | 6at1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 2 / Mutation: T82A Source method: isolated from a genetically manipulated source Details: ENZYME INHIBITED WITH MALIC ACID / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURBI / Plasmid: PEK233 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17113.600 Da / Num. of mol.: 2 / Mutation: T82A Source method: isolated from a genetically manipulated source Details: ENZYME INHIBITED WITH MALIC ACID / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURBI / Plasmid: PEK233 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase #3: Chemical | ChemComp-MLT / #4: Chemical | #5: 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: 3.3 Å3/Da / Density % sol: 59.03 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.85 Details: 7.5 MG/ML PROTEIN DIALYZED AGAINST 100MM MALIC ACID AT PH 5.85, | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.8 / Method: microdialysisDetails: Ke, H.M., (1984) Proc.Natl.Acad.Sci.U.S.A., 81, 4037. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→31.2 Å / Num. obs: 38085 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.2 / % possible all: 88.5 |
Reflection | *PLUS Num. all: 39763 / Num. obs: 37782 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: 6AT1 Resolution: 2.6→10 Å / Isotropic thermal model: ALL ATOMS / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 2
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Displacement parameters | Biso mean: 22.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.24 |