+Open data
-Basic information
Entry | Database: PDB / ID: 5mlp | ||||||
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Title | Structure of CDPS from Rickettsiella grylli | ||||||
Components | Uncharacterized protein | ||||||
Keywords | LIGASE / Cyclodipeptide Synthase | ||||||
Function / homology | Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / Uncharacterized protein Function and homology information | ||||||
Biological species | Rickettsiella grylli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Bourgeois, G. / Seguin, J. / Moutiez, M. / Babin, M. / Belin, P. / Mechulam, Y. / Gondry, M. / Schmitt, E. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2018 Title: Structural basis for partition of the cyclodipeptide synthases into two subfamilies. Authors: Bourgeois, G. / Seguin, J. / Babin, M. / Belin, P. / Moutiez, M. / Mechulam, Y. / Gondry, M. / Schmitt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mlp.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mlp.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mlp_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 5mlp_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 5mlp_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 5mlp_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/5mlp ftp://data.pdbj.org/pub/pdb/validation_reports/ml/5mlp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31486.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsiella grylli (bacteria) / Gene: RICGR_1344 / Production host: Escherichia coli (E. coli) / References: UniProt: A8PPN3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: PEG3350 15% Potassium fluoride 0.2M |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2016 | |||||||||
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.99→45.65 Å / Num. obs: 17008 / % possible obs: 98.5 % / Redundancy: 4.49 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7.02 | |||||||||
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.18 / CC1/2: 0.78 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NA Resolution: 1.99→40.427 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→40.427 Å
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Refine LS restraints |
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LS refinement shell |
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