+Open data
-Basic information
Entry | Database: PDB / ID: 4xlx | ||||||
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Title | Crystal structure of BjKS from Bradyrhizobium japonicum | ||||||
Components | Uncharacterized protein blr2150 | ||||||
Keywords | HYDROLASE / Diterpene synthases | ||||||
Function / homology | Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Uncharacterized protein blr2150 Function and homology information | ||||||
Biological species | Bradyrhizobium diazoefficiens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hu, Y. / Zheng, Y. / Ko, T.P. / Liu, W. / Guo, R.T. | ||||||
Citation | Journal: Sci Rep / Year: 2014 Title: Structure, function and inhibition of ent-kaurene synthase from Bradyrhizobium japonicum. Authors: Liu, W. / Feng, X. / Zheng, Y. / Huang, C.H. / Nakano, C. / Hoshino, T. / Bogue, S. / Ko, T.P. / Chen, C.C. / Cui, Y. / Li, J. / Wang, I. / Hsu, S.T. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xlx.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xlx.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xlx_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 4xlx_full_validation.pdf.gz | 481.6 KB | Display | |
Data in XML | 4xlx_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 4xlx_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/4xlx ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xlx | HTTPS FTP |
-Related structure data
Related structure data | 4w4rC 4w4sC 4xlyC 3w3f 3wbv C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33417.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria) Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: blr2150 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB (DE3) / References: UniProt: Q45222 #2: 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: 2.09 Å3/Da / Density % sol: 41.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1M ammonium tartrate dibasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 72234 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6728 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W3F 3w3f Resolution: 2→25 Å / Cross valid method: FREE R-VALUE / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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LS refinement shell | Resolution: 2→2.1 Å /
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