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- PDB-4a8h: Crystal structure of putrescine transcarbamylase from Enterococcu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a8h | ||||||
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Title | Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine | ||||||
![]() | PUTRESCINE CARBAMOYLTRANSFERASE | ||||||
![]() | TRANSFERASE / PAPU / AGMATINE DEIMINASE ROUTE / ORNITHINE / ORNITHINE ARGININE DEIMINASE / PHOSPHONOACETYLPUTRESCINE / PALO | ||||||
Function / homology | ![]() putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Polo, L.M. / Gil-Ortiz, F. / Rubio, V. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.5 KB | Display | ![]() |
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PDB format | ![]() | 229.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.9 KB | Display | ![]() |
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Full document | ![]() | 490 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a8pC ![]() 4a8tC ![]() 1a1sS C: citing same article ( 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper: (Code: given Matrix: (0.356, -0.934, -0.001), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40141.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q837U7, putrescine carbamoyltransferase |
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-Non-polymers , 6 types, 295 molecules ![](data/chem/img/PUW.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 125 MM AMMONIUM SULPHATE, 17% PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.43 MM N-(PHOSPHONOACETYL)PUTRESCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46 Å / Num. obs: 32509 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.3 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 2.5→20 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 9.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A1S Resolution: 2.5→29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.217 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.238 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.296 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29 Å
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Refine LS restraints |
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