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Yorodumi- PDB-4a8h: Crystal structure of putrescine transcarbamylase from Enterococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8h | ||||||
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Title | Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine | ||||||
Components | PUTRESCINE CARBAMOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PAPU / AGMATINE DEIMINASE ROUTE / ORNITHINE / ORNITHINE ARGININE DEIMINASE / PHOSPHONOACETYLPUTRESCINE / PALO | ||||||
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: 2.5 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 | 4a8h.cif.gz | 282.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8h.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a8h_validation.pdf.gz | 484.9 KB | Display | wwPDB validaton report |
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Full document | 4a8h_full_validation.pdf.gz | 490 KB | Display | |
Data in XML | 4a8h_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 4a8h_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8h ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8h | HTTPS FTP |
-Related structure data
Related structure data | 4a8pC 4a8tC 1a1sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: |
-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.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q837U7, putrescine carbamoyltransferase |
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-Non-polymers , 6 types, 295 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.91 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: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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