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Yorodumi- PDB-4a8t: Crystal structure of putrescine transcarbamylase from Enterococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8t | ||||||
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Title | Crystal structure of putrescine transcarbamylase from Enterococcus faecalis lacking its C-terminal Helix, with bound N5-(phosphonoacetyl) -L-ornithine | ||||||
Components | PUTRESCINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / TRABNSFERASE PALO / DELTA-N-(PHOSPHONOACETYL)-L-ORNITHINE / AGMATINE DEIMINASE ROUTE / AGMATINE CATABOLISM / AGMATINE FERMENTATION / ORNITHINE / ORNITHINE CARBAMOYLTRANSFERASE / ARGININE DEIMINASE / PHOSPHONOACETYLORNITHINE | ||||||
Function / homology | Function and homology information putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Polo, L.M. / Gil-Ortiz, F. / Rubio, V. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: New Insight Into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine Authors: Polo, L.M. / Gil-Ortiz, F. / Cantin, A. / Rubio, V. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a8t.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8t.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a8t_validation.pdf.gz | 724 KB | Display | wwPDB validaton report |
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Full document | 4a8t_full_validation.pdf.gz | 725.6 KB | Display | |
Data in XML | 4a8t_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4a8t_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8t ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8t | HTTPS FTP |
-Related structure data
Related structure data | 4a8hSC 4a8pC S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38377.277 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-317 Source method: isolated from a genetically manipulated source Details: THE PROTEIN LACKS THE C-TERMINAL HELIX / Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q837U7, putrescine carbamoyltransferase |
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#2: Chemical | ChemComp-PAO / |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-PGE / |
#5: Water | ChemComp-HOH / |
Sequence details | Y318 WAS REPLACED WITH A STOP CODON, LACKING THE C- TERMINAL HELIX |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.5 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M MAGNESIUM CHLORIDE, 30% POLYETHYLENE GLYCOL 400, 0.1 M HEPES, PH 7.5, 1 MM N5-(PHOSPHONOACETYL)-L-ORNITHINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→40 Å / Num. obs: 60518 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.59→30 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A8H Resolution: 1.59→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.15 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 76-78 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→30 Å
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Refine LS restraints |
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