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- PDB-8a3f: Proline Racemase (ProR) from the Gram-positive bacterium Acetoana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a3f | ||||||
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Title | Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic tetragonal data at 3.15 A | ||||||
![]() | Proline racemase A (AsProR) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Najmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii Authors: Najmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 496.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7pb3SC ![]() 8a4rC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37942.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DSMZ (Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH) Source: (gene. exp.) ![]() ![]() Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654 / Gene: prdF, CLOST_2228 / Details (production host): pET-29a / Production host: ![]() ![]() ![]() #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 51 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.15→109.1 Å / Num. obs: 11620 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.115 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.15→3.37 Å / Redundancy: 12.3 % / Rmerge(I) obs: 3.32 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2048 / CC1/2: 0.457 / Rpim(I) all: 1.335 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7pb3 Resolution: 3.15→77.707 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.875 / SU B: 127.441 / SU ML: 0.92 / Cross valid method: FREE R-VALUE / ESU R Free: 0.733 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 127.154 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→77.707 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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