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Yorodumi- PDB-7s8w: Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s8w | |||||||||||||||
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Title | Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q mutant in complex with N-succinylphenylglycine | |||||||||||||||
Components | N-succinylamino acid racemase/O-succinylbenzoate synthase | |||||||||||||||
Keywords | ISOMERASE / Complex / racemase / dehydratase / mutant | |||||||||||||||
Function / homology | Function and homology information O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Amycolatopsis sp. (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||||||||
Authors | Truong, D.P. / Rousseau, S. / Sacchettini, J.C. / Glasner, M.E. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Biochemistry / Year: 2021 Title: Second-Shell Amino Acid R266 Helps Determine N -Succinylamino Acid Racemase Reaction Specificity in Promiscuous N -Succinylamino Acid Racemase/ o -Succinylbenzoate Synthase Enzymes. Authors: Truong, D.P. / Rousseau, S. / Machala, B.W. / Huddleston, J.P. / Zhu, M. / Hull, K.G. / Romo, D. / Raushel, F.M. / Sacchettini, J.C. / Glasner, M.E. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s8w.cif.gz | 310.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s8w.ent.gz | 231.9 KB | Display | PDB format |
PDBx/mmJSON format | 7s8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/7s8w ftp://data.pdbj.org/pub/pdb/validation_reports/s8/7s8w | HTTPS FTP |
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-Related structure data
Related structure data | 1sjbS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 39419.203 Da / Num. of mol.: 4 / Mutation: R266Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Gene: Aaar, menC / Production host: Escherichia coli (E. coli) / References: UniProt: Q44244, o-succinylbenzoate synthase #2: Chemical | ChemComp-8JI / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | 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: 3.53 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 28% PEG 4000 0.1 M Tris (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 49028 / % possible obs: 99.89 % / Redundancy: 6.8 % / Biso Wilson estimate: 66 Å2 / Rrim(I) all: 0.185 / Net I/σ(I): 8.64 |
Reflection shell | Resolution: 2.93→3 Å / Redundancy: 2.1 % / Num. unique obs: 4865 / CC1/2: 0.759 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SJB Resolution: 2.9→49.8 Å / SU ML: 0.3254 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5588 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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