[English] 日本語
Yorodumi- PDB-8a3f: Proline Racemase (ProR) from the Gram-positive bacterium Acetoana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a3f | ||||||
---|---|---|---|---|---|---|---|
Title | Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii from isotropic tetragonal data at 3.15 A | ||||||
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 DSM 519 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Najmudin, S. / Pan, X.-S. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R. | ||||||
Funding support | United Kingdom, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8a3f.cif.gz | 496.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8a3f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a3f_validation.pdf.gz | 808.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8a3f_full_validation.pdf.gz | 880.8 KB | Display | |
Data in XML | 8a3f_validation.xml.gz | 31 KB | Display | |
Data in CIF | 8a3f_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a3f ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a3f | HTTPS FTP |
-Related structure data
Related structure data | 7pb3SC 8a4rC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 DSM 519 (bacteria) Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654 / Gene: prdF, CLOST_2228 / Details (production host): pET-29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): lambdaDE3 pLysS / References: UniProt: E3PTZ4 #2: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 51 % |
---|---|
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 |
---|---|
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: 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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→77.707 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|