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Yorodumi- PDB-7zr3: STRUCTURE OF ESTER-HYDROLASE EH0 FROM THE METAGENOME OF SORGHUM B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zr3 | ||||||
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Title | STRUCTURE OF ESTER-HYDROLASE EH0 FROM THE METAGENOME OF SORGHUM BICOLOR RHIZOSPHERE FROM THE HENFAES RESEARCH CENTRE (GWYNEDD, WALES) | ||||||
Components | EH0 | ||||||
Keywords | HYDROLASE / ester hydrolase | ||||||
Function / homology | ACETATE ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Cea-Rama, I. / Sanz-Aparicio, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Appl.Environ.Microbiol. / Year: 2023 Title: The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome. Authors: Distaso, M. / Cea-Rama, I. / Coscolin, C. / Chernikova, T.N. / Tran, H. / Ferrer, M. / Sanz-Aparicio, J. / Golyshin, P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zr3.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zr3.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zr3_validation.pdf.gz | 467.1 KB | Display | wwPDB validaton report |
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Full document | 7zr3_full_validation.pdf.gz | 470.1 KB | Display | |
Data in XML | 7zr3_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 7zr3_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/7zr3 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/7zr3 | HTTPS FTP |
-Related structure data
Related structure data | 4ypvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36748.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 5 types, 440 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.27 Å3/Da / Density % sol: 62.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 11% PEG8000, 100mM Bis-Tris pH 5.5, 100mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07218 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2017 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07218 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→64.36 Å / Num. obs: 64849 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4496 / CC1/2: 0.92 / Rpim(I) all: 0.219 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPV Resolution: 2.01→64.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.145 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.58 Å2 / Biso mean: 43.042 Å2 / Biso min: 20.39 Å2
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Refinement step | Cycle: final / Resolution: 2.01→64.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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