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- PDB-1gbn: HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gbn | ||||||
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Title | HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE | ||||||
![]() | ORNITHINE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE / ORNITHINE AMINOTRANSFERASE / UREA CYCLE / PYRIDOXAL-5'-PHOSPHATE | ||||||
Function / homology | ![]() arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shah, S.A. / Shen, B.W. / Brunger, A.T. | ||||||
![]() | ![]() Title: Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition. Authors: Shah, S.A. / Shen, B.W. / Brunger, A.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 288.7 KB | Display | ![]() |
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PDB format | ![]() | 232.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 509 KB | Display | |
Data in XML | ![]() | 49.2 KB | Display | |
Data in CIF | ![]() | 68 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2canC ![]() 1oatS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 44706.156 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: BOUND INHIBITOR GABACULINE / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GAB / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 50.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 10, 1995 / Details: DUEL SLITS |
Radiation | Monochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9417 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 57010 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.17 / % possible all: 80.1 |
Reflection | *PLUS % possible obs: 89.9 % |
Reflection shell | *PLUS Lowest resolution: 2.4 Å / % possible obs: 80.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.171 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OAT Resolution: 2.3→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 470426.53 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 1.618 Å2 / Rms dev position: 0.1647 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 52218 / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. reflection Rfree: 70 / % reflection Rfree: 10 % / Num. reflection Rwork: 5123 |