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- PDB-2otc: ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-O... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2otc | ||||||
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Title | ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-ORNITHINE | ||||||
![]() | ORNITHINE CARBAMOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / OTCASE / ORNITHINE / TRANSCARBAMOYLASE / ARGININE SYNTHESIS / UREA CYCLE | ||||||
Function / homology | ![]() ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ha, Y. / Allewell, N.M. | ||||||
![]() | ![]() Title: Substrate-induced conformational change in a trimeric ornithine transcarbamoylase. Authors: Ha, Y. / McCann, M.T. / Tuchman, M. / Allewell, N.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 568.6 KB | Display | ![]() |
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PDB format | ![]() | 474.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1otcS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 36888.953 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: N-(PHOSPHONACETYL)-L-ORNITHINE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PAO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 14% PEG 4K, 90MM NA ACETATE, 70MM MGCL2, 2% MPD, 45% TRIS-HCL PH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1997 / Details: NO |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 53778 / % possible obs: 58 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 9.73 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.13 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.262 / Rsym value: 0.208 / % possible all: 20 |
Reflection shell | *PLUS % possible obs: 20 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OTC Resolution: 2.8→15 Å / Data cutoff high absF: 40 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.93 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.327 |