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Open data
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Basic information
Entry | Database: PDB / ID: 1aw8 | |||||||||
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Title | PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE | |||||||||
![]() | (L-ASPARTATE-ALPHA-DECARBOXYLASE) x 2 | |||||||||
![]() | DECARBOXYLASE / PANTOTHENATE PATHWAY / LYASE / PROTEIN SELF-PROCESSING | |||||||||
Function / homology | ![]() alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.2 KB | Display | ![]() |
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Full document | ![]() | 382.1 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: |
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Components
#1: Protein/peptide | Mass: 2841.380 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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: ![]() | |||||||||||||||||||||
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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