+Open data
-Basic information
Entry | Database: PDB / ID: 1aw8 | |||||||||
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Title | PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE | |||||||||
Components | (L-ASPARTATE-ALPHA-DECARBOXYLASE) x 2 | |||||||||
Keywords | DECARBOXYLASE / PANTOTHENATE PATHWAY / LYASE / PROTEIN SELF-PROCESSING | |||||||||
Function / homology | Function and homology information alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | |||||||||
Authors | Albert, A. / Dhanaraj, V. / Genschel, U. / Khan, G. / Ramjee, M.K. / Pulido, R. / Sybanda, B.L. / von Delf, F. / Witty, M. / Blundell, T.L. ...Albert, A. / Dhanaraj, V. / Genschel, U. / Khan, G. / Ramjee, M.K. / Pulido, R. / Sybanda, B.L. / von Delf, F. / Witty, M. / Blundell, T.L. / Smith, A.G. / Abell, C. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing. Authors: Albert, A. / Dhanaraj, V. / Genschel, U. / Khan, G. / Ramjee, M.K. / Pulido, R. / Sibanda, B.L. / von Delft, F. / Witty, M. / Blundell, T.L. / Smith, A.G. / Abell, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aw8.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aw8.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/1aw8 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/1aw8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.764933, 0.394656, -0.509043), Vector: |
-Components
#1: Protein/peptide | Mass: 2841.380 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A790, aspartate 1-decarboxylase #2: Protein | Mass: 9872.942 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: microheterogeneity at residue B25 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A790, aspartate 1-decarboxylase #3: 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: 3.2 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 2000 MME, 0.1 M NA ACETATE, PH 4.6 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.488 |
Detector | Date: Jul 31, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.6 Å / Num. obs: 16129 / % possible obs: 98 % / Observed criterion σ(I): 2.2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.6 / % possible all: 80 |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.2 Details: THE ELECTRON DENSITY FOR RESIDUES 20 - 25 DIFFERS IN THE TWO PROTOMERS IN THE ASYMMETRIC UNIT. THE FIRST PROTOMER (CHAINS D AND E) SHOWS CLEAR INDICATION FOR A PYRUVOYL GROUP. IN THE SECOND ...Details: THE ELECTRON DENSITY FOR RESIDUES 20 - 25 DIFFERS IN THE TWO PROTOMERS IN THE ASYMMETRIC UNIT. THE FIRST PROTOMER (CHAINS D AND E) SHOWS CLEAR INDICATION FOR A PYRUVOYL GROUP. IN THE SECOND (CHAINS A AND B), ELECTRON DENSITY INDICATES TWO SUPERPOSED STRUCTURES OF EQUAL OCCUPANCY, ONE CORRESPONDING TO A PYRUVOYL GROUP (RESIDUE PVL) AND THE OTHER (RESIDUE SEG) CORRESPONDING TO AN ESTER INTERMEDIATE IN THE FORMATION OF THE PYRUVOYL GROUP. HET GROUP SEG LINKS CHAINS A AND B. BECAUSE OF PDB FORMAT LIMITATIONS ONLY PVL APPEARS ON SEQRES. THE ELECTRON DENSITY FOR RESIDUES 20 - 25 DIFFERS IN THE TWO PROTOMERS IN THE ASYMMETRIC UNIT. THE FIRST PROTOMER (CHAINS D AND E) SHOWS CLEAR INDICATION FOR A PYRUVOYL GROUP. IN THE SECOND (CHAINS A AND B), ELECTRON DENSITY INDICATES TWO SUPERPOSED STRUCTURES OF EQUAL OCCUPANCY, ONE CORRESPONDING TO A PYRUVOYL GROUP (RESIDUE PVL) AND THE OTHER (RESIDUE SEG) CORRESPONDING TO AN ESTER INTERMEDIATE IN THE FORMATION OF THE PYRUVOYL GROUP. HET GROUP SEG LINKS CHAINS A AND B. BECAUSE OF PDB FORMAT LIMITATIONS ONLY PVL APPEARS ON SEQRES.
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 7 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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