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Yorodumi- PDB-7xrv: Bacteroides thetaiotaomicron ferulic acid esterase - S150A (BT_40... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xrv | ||||||
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Title | Bacteroides thetaiotaomicron ferulic acid esterase - S150A (BT_4077-S150A) complex with trans-methylferulate | ||||||
Components | Ferulic acid esterase | ||||||
Keywords | HYDROLASE / Esterase / Complex | ||||||
Function / homology | Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Alpha/Beta hydrolase fold / Trans-methylferulate / Endo-1,4-beta-xylanase Z Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.713 Å | ||||||
Authors | Du, G.M. / Wang, Y.L. / Xin, F.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Insights into the regulatory mechanism of BtFae activity by oligomerization and a distinct substrate binding pocket adjacent to the active site Authors: Du, G.M. / Wang, Y.L. / Xin, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xrv.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7xrv.ent.gz | 898.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xrv_validation.pdf.gz | 758.7 KB | Display | wwPDB validaton report |
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Full document | 7xrv_full_validation.pdf.gz | 716.3 KB | Display | |
Data in XML | 7xrv_validation.xml.gz | 95.1 KB | Display | |
Data in CIF | 7xrv_validation.cif.gz | 127.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/7xrv ftp://data.pdbj.org/pub/pdb/validation_reports/xr/7xrv | HTTPS FTP |
-Related structure data
Related structure data | 7xrtSC 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: 33323.828 Da / Num. of mol.: 10 / Mutation: S150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_4077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0E4 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SZQ / #4: 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: 3.03 Å3/Da / Density % sol: 59.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.16 M succinic acid (pH 7.0), 16% (w/v) PEG3350, 0.2 M sodium iodide, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 9, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.71→109.86 Å / Num. obs: 101667 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.958 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.08 / Rrim(I) all: 0.241 / Net I/σ(I): 10.8 / Num. measured all: 969467 / Scaling rejects: 4427 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XRT Resolution: 2.713→109.859 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.02 / Stereochemistry target values: ML
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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 max: 130.44 Å2 / Biso mean: 43.7279 Å2 / Biso min: 8.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.713→109.859 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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