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- PDB-6wpm: Crystal structure of a putative oligosaccharide periplasmic-bindi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wpm | |||||||||
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Title | Crystal structure of a putative oligosaccharide periplasmic-binding protein from Synechococcus sp. MITs9220 in complex with zinc | |||||||||
![]() | Substrate-binding protein | |||||||||
![]() | TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / sugar-binding protein | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ford, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. Authors: Ford, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.3 KB | Display | ![]() |
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PDB format | ![]() | 203.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47341.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 20 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulphate (2 M), PEG 3350 (20% w/v) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 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: 2.23→53.42 Å / Num. obs: 13405 / % possible obs: 99.43 % / Redundancy: 3.8 % / Biso Wilson estimate: 86.28 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 0.0694 |
Reflection shell | Resolution: 2.88→2.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.027 / Mean I/σ(I) obs: 30 / Num. unique obs: 1253 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→45.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 55.9373651946 Å / Origin y: 25.8361144798 Å / Origin z: 26.0606700515 Å
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Refinement TLS group | Selection details: all |