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Yorodumi- PDB-7pb3: Structural and Functional analysis of the Proline Racemase (ProR)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pb3 | ||||||
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Title | Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii | ||||||
Components | Proline racemase A (AsProR) | ||||||
Keywords | ISOMERASE / pyridoxal 5-phosphate-independent racemase / diaminopimelate epimerase-like (DAPE) fold / stereo inversion / pyrrole 2-carboxylate / Gram-positive bacterium | ||||||
Function / homology | proline racemase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / PYRROLE-2-CARBOXYLATE / Proline racemase Function and homology information | ||||||
Biological species | Acetoanaerobium sticklandii | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å | ||||||
Authors | Najmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pb3.cif.gz | 492 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pb3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pb3_validation.pdf.gz | 851.2 KB | Display | wwPDB validaton report |
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Full document | 7pb3_full_validation.pdf.gz | 885.5 KB | Display | |
Data in XML | 7pb3_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 7pb3_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/7pb3 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/7pb3 | HTTPS FTP |
-Related structure data
Related structure data | 8a3fC 8a4rC 6j7cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654) (bacteria) Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654 / Gene: prdF, CLOST_2228 / Plasmid: pET-29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): lambdaDE3 pLysS / References: UniProt: E3PTZ4 #2: Chemical | Has ligand of interest | Y | |
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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: 2.52 Å3/Da / Density % sol: 51 % Description: Initial hits were obtained within a week. Subsequently improved by streak seeding and further optimisation screens around hit condition |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
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: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→109.1 Å / Num. obs: 9545 / % possible obs: 89.7 % / Redundancy: 12.6 % / Biso Wilson estimate: 109.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.046 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.84→3.29 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.877 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 734 / CC1/2: 0.584 / Rpim(I) all: 0.769 / % possible all: 68.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6j7c Resolution: 2.841→77.223 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.334 / WRfactor Rwork: 0.243 / SU B: 56.225 / SU ML: 0.534 / Average fsc free: 0.754 / Average fsc work: 0.804 / Cross valid method: FREE R-VALUE / ESU R Free: 0.853 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: 126.233 Å2
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Refinement step | Cycle: LAST / Resolution: 2.841→77.223 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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