+Open data
-Basic information
Entry | Database: PDB / ID: 8hlf | ||||||
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Title | Crystal structure of DddK-DMSOP complex | ||||||
Components | Novel protein with potential Cupin domain | ||||||
Keywords | LYASE / DMSOP lyase / complex | ||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / outer membrane-bounded periplasmic space / metal ion binding / Chem-LNI / : / Novel protein with potential Cupin domain Function and homology information | ||||||
Biological species | Candidatus Pelagibacter ubique HTCC1062 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Peng, M. / Li, C.Y. / Zhang, Y.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms. Authors: Carrion, O. / Li, C.Y. / Peng, M. / Wang, J. / Pohnert, G. / Azizah, M. / Zhu, X.Y. / Curson, A.R.J. / Wang, Q. / Walsham, K.S. / Zhang, X.H. / Monaco, S. / Harvey, J.M. / Chen, X.L. / Gao, ...Authors: Carrion, O. / Li, C.Y. / Peng, M. / Wang, J. / Pohnert, G. / Azizah, M. / Zhu, X.Y. / Curson, A.R.J. / Wang, Q. / Walsham, K.S. / Zhang, X.H. / Monaco, S. / Harvey, J.M. / Chen, X.L. / Gao, C. / Wang, N. / Wang, X.J. / Wang, P. / Giovanonni, S.J. / Lee, C.P. / Suffridge, C.P. / Zhang, Y. / Luo, Z. / Wang, D. / Todd, J.D. / Zhang, Y.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hlf.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hlf.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hlf_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 8hlf_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 8hlf_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8hlf_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/8hlf ftp://data.pdbj.org/pub/pdb/validation_reports/hl/8hlf | HTTPS FTP |
-Related structure data
Related structure data | 8hleC 6a53S 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: 15177.058 Da / Num. of mol.: 2 / Mutation: Y64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Pelagibacter ubique HTCC1062 (bacteria) Gene: SAR11_0394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FNM4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: SPG buffer, PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→26.66 Å / Num. obs: 28768 / % possible obs: 98.35 % / Redundancy: 3.4 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.62→1.678 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 2802 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.121 / Rrim(I) all: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A53 Resolution: 1.62→26.66 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→26.66 Å
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Refine LS restraints |
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LS refinement shell |
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