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Yorodumi- PDB-6lk3: The Functional Characterization and Crystal Structure of Type II ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lk3 | ||||||
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Title | The Functional Characterization and Crystal Structure of Type II Peptidyl Carrier Protein ColA1a in Collismycins Biosynthesis | ||||||
Components | Putative free-standing acyl carrier protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Biosynthesis / ColA1a / Collismycins / NRPS / Peptidyl Carrier Protein | ||||||
Function / homology | Phosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / Putative free-standing acyl carrier protein Function and homology information | ||||||
Biological species | Streptomyces sp. CS40 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Ma, X.Y. / Wang, G.Y. / Liu, T. / Chi, C.B. / Zhang, Z.Y. / Yang, D.H. / Liu, W. / Ma, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Chin.J.Chem. / Year: 2020 Title: The functional characterization and crystal structure of type II peptidyl carrier protein ColA1a in collismycins biosynthesis. Authors: Ma, X.Y. / Wang, G.Y. / Liu, T. / Chi, C.B. / Zhang, Z.Y. / Yang, D.H. / Liu, W. / Ma, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lk3.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lk3.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 6lk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lk3_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 6lk3_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 6lk3_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 6lk3_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lk3 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lk3 | 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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-Components
#1: Protein | Mass: 11883.458 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CS40 (bacteria) / Gene: clmP / Production host: Escherichia coli (E. coli) / References: UniProt: H1ZYT7 #2: Water | ChemComp-HOH / | Sequence details | The source organism is Streptomyces roseosporus NRRL 11379. So, There is no genome sequence of ...The source organism is Streptomyces roseosporus NRRL 11379. So, There is no genome sequence of Streptomyces roseosporus NRRL 11379 in the database. | |
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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: 1.78 Å3/Da / Density % sol: 30.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.25, 25% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.51 Å / Num. obs: 9816 / % possible obs: 98.1 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 503 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→39.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.852 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.45 Å2 / Biso mean: 24.982 Å2 / Biso min: 9.64 Å2
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Refinement step | Cycle: final / Resolution: 2.1→39.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Rfactor Rfree error: 0
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