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Yorodumi- PDB-6rb0: STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rb0 | |||||||||
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Title | STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF METHYL 4-NITROPHENYL HEXYLPHOSPHONATE | |||||||||
Components | EH1AB1 | |||||||||
Keywords | HYDROLASE / Ester Hydrolase / Complex | |||||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / methyl hydrogen (R)-hexylphosphonate Function and homology information | |||||||||
Biological species | metagenome (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Cea-Rama, I. / Sanz-Aparicio, J. | |||||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Catal / Year: 2020 Title: Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis Authors: Alonso, S. / Santiago, G. / Cea-Rama, I. / Fernandez-Lopez, L. / Coscolin, C. / Modregger, J. / Ressmann, A.K. / Martinez-Martinez, M. / Marrero, H. / Bargiela, R. / Pita, M. / Gonzalez- ...Authors: Alonso, S. / Santiago, G. / Cea-Rama, I. / Fernandez-Lopez, L. / Coscolin, C. / Modregger, J. / Ressmann, A.K. / Martinez-Martinez, M. / Marrero, H. / Bargiela, R. / Pita, M. / Gonzalez-Alfonso, J.L. / Briand, M.L. / Rojo, D. / Barbas, C. / Plou, F.J. / Golyshin, P.N. / Shahgaldian, P. / Sanz-Aparicio, J. / Guallar, V. / Ferrer, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rb0.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rb0.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rb0_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 6rb0_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | 6rb0_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 6rb0_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rb0 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rb0 | HTTPS FTP |
-Related structure data
Related structure data | 6i8fSC 6rkyC S: Starting model for refinement C: citing same article (ref.) |
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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: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 1 - 315 / Label seq-ID: 15 - 329
NCS ensembles : (Details: A, B) |
-Components
#1: Protein | Mass: 35603.793 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) #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MHH / #4: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.2M NaF |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97936 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2018 / 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: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→43.04 Å / Num. obs: 29764 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.84 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.069 / Rrim(I) all: 0.164 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2895 / CC1/2: 0.818 / Rpim(I) all: 0.296 / Rrim(I) all: 0.712 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I8F Resolution: 2.35→43.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.471 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.735 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→43.04 Å
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Refine LS restraints |
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