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Yorodumi- PDB-5msp: Structure of the unmodified PCP-R didomain of carboxylic acid red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5msp | ||||||
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Title | Structure of the unmodified PCP-R didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADP, F2221 form | ||||||
Components | Thioester reductase domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / adenylation domain / carboxylic acid reductase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / organonitrogen compound biosynthetic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / phosphopantetheine binding / lipid metabolic process / NADP binding / ATP binding Similarity search - Function | ||||||
Biological species | Segniliparus rugosus ATCC BAA-974 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Gahloth, D. / Leys, D. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis. Authors: Gahloth, D. / Dunstan, M.S. / Quaglia, D. / Klumbys, E. / Lockhart-Cairns, M.P. / Hill, A.M. / Derrington, S.R. / Scrutton, N.S. / Turner, N.J. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5msp.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5msp.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 5msp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/5msp ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5msp | HTTPS FTP |
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-Related structure data
Related structure data | 5mscC 5msdC 5msoSC 5msrC 5mssC 5mstC 5msuC 5msvC 5mswC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 128368.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Segniliparus rugosus ATCC BAA-974 (bacteria) Gene: HMPREF9336_01297 / Production host: Escherichia coli (E. coli) / References: UniProt: E5XP76 |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: CARsr PCP-Red crystals were obtained in 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→101.04 Å / Num. obs: 36214 / % possible obs: 99 % / Redundancy: 5.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.41→2.5 Å / CC1/2: 0.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MSO Resolution: 2.41→101.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.887 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.19 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.76 Å2
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Refinement step | Cycle: 1 / Resolution: 2.41→101.04 Å
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Refine LS restraints |
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