+Open data
-Basic information
Entry | Database: PDB / ID: 1akm | ||||||
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Title | ORNITHINE TRANSCARBAMYLASE FROM ESCHERICHIA COLI | ||||||
Components | ORNITHINE TRANSCARBAMYLASE | ||||||
Keywords | TRANSFERASE / ANABOLIC / UREA CYCLE / CARBAMYL PHOSPHATE | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT, SIRAS / Resolution: 2.8 Å | ||||||
Authors | Head, J.F. / Seaton, B. / Jin, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure at 2.8 A resolution of anabolic ornithine transcarbamylase from Escherichia coli. Authors: Jin, L. / Seaton, B.A. / Head, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1akm.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1akm.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 1akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1akm | HTTPS FTP |
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-Related structure data
Related structure data | 2at2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36818.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARGI / Plasmid: PUC18 / Gene (production host): ARGI / Production host: Escherichia coli (E. coli) / Strain (production host): TB2 / Variant (production host): DELTA ARGI-PYRB, ARGF- / References: UniProt: P04391, ornithine carbamoyltransferase |
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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: 2.5 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALLIZED FROM 20% PEG 4000, 10% MPD, 1MM MGSO4, 50MM HEPES, PH 7.5. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→90 Å / Num. obs: 25858 / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, SIRAS Starting model: PDB ENTRY 2AT2 Resolution: 2.8→6 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |