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Yorodumi- PDB-7q4j: A thermostable lipase from Thermoanaerobacter thermohydrosulfuric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q4j | ||||||
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Title | A thermostable lipase from Thermoanaerobacter thermohydrosulfuricus in complex a monoacylglycerol intermediate | ||||||
Components | (Serine aminopeptidase S33 domain-containing ...) x 2 | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE / THERMOSTABLE / monoacylglycerol / lipase | ||||||
Function / homology | Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / DECANE / nonane / N-OCTANE / STEARIC ACID / Serine aminopeptidase S33 domain-containing protein Function and homology information | ||||||
Biological species | Thermoanaerobacter thermohydrosulfuricus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å | ||||||
Authors | Pinotsis, N. / Wilmanns, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex. Authors: Pinotsis, N. / Kruger, A. / Tomas, N. / Chatziefthymiou, S.D. / Litz, C. / Mortensen, S.A. / Daffe, M. / Marrakchi, H. / Antranikian, G. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q4j.cif.gz | 279.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q4j.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q4j_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7q4j_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7q4j_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 7q4j_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4j ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4j | HTTPS FTP |
-Related structure data
Related structure data | 7q4hC 8b9sC 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
-Serine aminopeptidase S33 domain-containing ... , 2 types, 2 molecules AB
#1: Protein | Mass: 29960.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Methylates Lysines, Seleno-methionines Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria) Gene: SAMN04244560_02687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7VV58 |
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#2: Protein | Mass: 30040.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria) Gene: SAMN04244560_02687 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7VV58 |
-Non-polymers , 8 types, 305 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-DD9 / | #9: Chemical | ChemComp-D10 / | #10: Water | ChemComp-HOH / | |
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-Details
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: 2.75 Å3/Da / Density % sol: 55.26 % / Description: parallelepiped of about 50 x 50 x 100 micro-m |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.4 M ammonium sulfate, 0.1 M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97873, 0.97903 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2009 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.91→20 Å / Num. obs: 49383 / % possible obs: 97.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.26 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.4 | |||||||||
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2071 / CC1/2: 0.99 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.91→19.75 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5375 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→19.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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