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- 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 | ||||||
![]() | PUTRESCINE CARBAMOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / PALO / DELTA-N-(PHOSPHONOACETYL)-L-ORNITHINE / AGMATINE DEIMINASE ROUTE / ORNITHINE CARBAMOYLTRANSFERASE / ARGININE DEIMINASE / PHOSPHONOACETYLORNITHINE | ||||||
Function / homology | ![]() putrescine 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 | ![]() ![]() ![]() | ||||||
![]() | Polo, L.M. / Rubio, V. | ||||||
![]() | ![]() Title: Curing a Mutant Transcarbamylase with a Small Molecule: A Crystallographic View Authors: Polo, L.M. / Rubio, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 779 KB | Display | ![]() |
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PDB format | ![]() | 649.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 77 KB | Display | |
Data in CIF | ![]() | 108.3 KB | Display | |
Arichive directory | ![]() ![]() | 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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1 | ![]()
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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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() Starting 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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