[English] 日本語
Yorodumi- PDB-4am8: Crystal structure of the R54G mutant of putrescine transcarbamyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4am8 | ||||||
---|---|---|---|---|---|---|---|
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 information putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Polo, L.M. / Rubio, V. | ||||||
Citation | Journal: To be Published Title: Curing a Mutant Transcarbamylase with a Small Molecule: A Crystallographic View Authors: Polo, L.M. / Rubio, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4am8.cif.gz | 779 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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
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 |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-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.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q837U7, putrescine carbamoyltransferase |
---|
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE |
---|---|
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 |
---|---|
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|