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Yorodumi- PDB-2otc: ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2otc | ||||||
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Title | ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-ORNITHINE | ||||||
Components | ORNITHINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / OTCASE / ORNITHINE / TRANSCARBAMOYLASE / ARGININE SYNTHESIS / UREA CYCLE | ||||||
Function / homology | Function and homology information 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 | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ha, Y. / Allewell, N.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2otc.cif.gz | 568.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2otc.ent.gz | 474.1 KB | Display | PDB format |
PDBx/mmJSON format | 2otc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2otc_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 2otc_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 2otc_validation.xml.gz | 108.1 KB | Display | |
Data in CIF | 2otc_validation.cif.gz | 143.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/2otc ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2otc | HTTPS FTP |
-Related structure data
Related structure data | 1otcS 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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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.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 (DE3) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: ARGI / Plasmid: PET-ARGI / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): ARGI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04391, ornithine carbamoyltransferase #2: Chemical | ChemComp-PAO / #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: 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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.327 |