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- PDB-3h4w: Structure of a Ca+2 dependent Phosphatidylinositol-specific phosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h4w | ||||||
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Title | Structure of a Ca+2 dependent Phosphatidylinositol-specific phospholipase C (PI-PLC) Enzyme from Streptomyces antibioticus | ||||||
![]() | Phosphatidylinositol-specific phospholipase C1 | ||||||
![]() | HYDROLASE / PI-PLC / Ca2+-dependent / catalytic TIM barrel / disulfide-linked helix-loop | ||||||
Function / homology | ![]() phosphoinositide phospholipase C / phosphatidylinositol phospholipase C activity / lipid metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, M.R. / Selby, T.L. | ||||||
![]() | ![]() Title: Crystal Structure of a Ca2+-dependent PI-PLC Authors: Jackson, M.R. / Selby, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 468.8 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.8 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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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: 36867.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal aa sequence in the gene (1.mngkrcvgtasraaaaviavsgpaga.26) is cleaved off by the organism and was replaced with the HIS-tagged sequence (1.MGSSHHHHHHSSGLVPRGSHM.21) for protein ...Details: The N-terminal aa sequence in the gene (1.mngkrcvgtasraaaaviavsgpaga.26) is cleaved off by the organism and was replaced with the HIS-tagged sequence (1.MGSSHHHHHHSSGLVPRGSHM.21) for protein expression. Selenomethionine incorporation using auxotrophic strain and synthetically substituted media. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B3A043, phosphoinositide phospholipase C |
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-Non-polymers , 5 types, 328 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/ACE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-EOH / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE RESIDUE 264 IN COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of ...Details: 21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of macroseedings with derivatized enzyme and same conditions., VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Protocol: SAD / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→77.61 Å / Num. all: 52173 / Num. obs: 52171 / % possible obs: 95.15 % / Observed criterion σ(I): 3.7 / Redundancy: 11.65 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.2689 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.76 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.19 / Num. measured all: 36537 / Num. unique all: 6345 / % possible all: 81.66 |
-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Processing
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Refinement | Method to determine structure: ![]() 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.16 Å2 / Biso mean: 14.295 Å2 / Biso min: 6.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→77.59 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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