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Yorodumi- PDB-4am8: Crystal structure of the R54G mutant of putrescine transcarbamyla... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4am8 | ||||||
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| Title | Crystal structure of the R54G mutant of putrescine transcarbamylase from Enterococcus faecalis bound to a curing guanidinium ion | ||||||
Components | PUTRESCINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PALO / DELTA-N-(PHOSPHONOACETYL)-L-ORNITHINE / AGMATINE DEIMINASE ROUTE / ORNITHINE CARBAMOYLTRANSFERASE / ARGININE DEIMINASE / PHOSPHONOACETYLORNITHINE | ||||||
| Function / homology | Function and homology informationputrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / amino acid binding / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Polo, L.M. / Rubio, V. | ||||||
Citation | Journal: To be PublishedTitle: Curing a Mutant Transcarbamylase with a Small Molecule: A Crystallographic View Authors: Polo, L.M. / Rubio, V. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4am8.cif.gz | 779 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4am8.ent.gz | 649.5 KB | Display | PDB format |
| PDBx/mmJSON format | 4am8.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4am8_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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| Full document | 4am8_full_validation.pdf.gz | 2 MB | Display | |
| Data in XML | 4am8_validation.xml.gz | 77 KB | Display | |
| Data in CIF | 4am8_validation.cif.gz | 108.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4am8 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am8 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4a8pS 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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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 6 molecules ABCDEF
| #1: Protein | Mass: 40041.254 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q837U7, putrescine carbamoyltransferase |
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-Non-polymers , 7 types, 848 molecules 












| #2: Chemical | | #3: Chemical | ChemComp-PAO / #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-TRS / #6: Chemical | #7: Chemical | ChemComp-ILE / | #8: 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: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE |
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| Crystal grow | pH: 7.5 Details: 0.02 M MAGNESIUM CHLORIDE, 30 % PEG 550 MONOMETHYLETHER, 0.1 M HEPES PH 7.5, 0.001 M PALO, 0.05 M GUANIDINIUM CHLORIDE |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
| Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 19, 2010 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
| Reflection | Resolution: 1.99→41 Å / Num. obs: 130385 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.6 |
| Reflection shell | Resolution: 2→30 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 82 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4A8P Resolution: 1.99→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.73 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 25.913 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.99→25 Å
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| Refine LS restraints |
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