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Yorodumi- PDB-1u0m: Crystal Structure of 1,3,6,8-Tetrahydroxynaphthalene Synthase (TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u0m | ||||||
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Title | Crystal Structure of 1,3,6,8-Tetrahydroxynaphthalene Synthase (THNS) from Streptomyces coelicolor A3(2): a Bacterial Type III Polyketide Synthase (PKS) Provides Insights into Enzymatic Control of Reactive Polyketide Intermediates | ||||||
Components | putative polyketide synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / type III polyketide synthase / PKS / bacterial / thiolase fold / alpha-beta-alpha-beta-alpha fold / catalytic triad / CHS-like / THNS / tetrahydroxynaphthalene synthase / chalcone/stilbene synthase superfamily / malonyl-CoA | ||||||
Function / homology | Function and homology information 1,3,6,8-tetrahydroxynaphthalene synthase / melanin biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, AB INITIO PHASING / Resolution: 2.22 Å | ||||||
Authors | Austin, M.B. / Izumikawa, M. / Bowman, M.E. / Udwary, D.W. / Ferrer, J.L. / Moore, B.S. / Noel, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates Authors: Austin, M.B. / Izumikawa, M. / Bowman, M.E. / Udwary, D.W. / Ferrer, J.L. / Moore, B.S. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0m.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0m.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u0m_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 1u0m_full_validation.pdf.gz | 810.9 KB | Display | |
Data in XML | 1u0m_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 1u0m_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0m ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0m | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Chains A and B constitute the biological homodimeric assembly |
-Components
#1: Protein | Mass: 41669.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO1206 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9FCA7 #2: Chemical | #3: Chemical | #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: 2.7 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, Magnesium chloride, Na+MOPSO- buffer, sucrose, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.0718,1.0713,0.9050 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 2001 | ||||||||||||
Radiation | Monochromator: Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→40.4 Å / Num. all: 37126 / Num. obs: 37126 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.7 Å2 | ||||||||||||
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 42.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, AB INITIO PHASING / Resolution: 2.22→40.39 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3024240.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Initial low-resolution experimental phases obtained using SOLVE and a separate 2.9 Angstrom Pt-derivative MAD data set. A THNS homology model (based on CHS structure) was then manually fit ...Details: Initial low-resolution experimental phases obtained using SOLVE and a separate 2.9 Angstrom Pt-derivative MAD data set. A THNS homology model (based on CHS structure) was then manually fit and rebuilt into the resulting 3.9 Angstrom electron density. This rebuilt model was subsequently refined only against the higher 2.2 Angstrom native data set deposited here.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.0123 Å2 / ksol: 0.374354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→40.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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