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Open data
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Basic information
Entry | Database: PDB / ID: 8fmc | |||||||||
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Title | Crystal Structure of Kemp Eliminase 1A53-core in unbound state | |||||||||
![]() | Kemp Eliminase 1A53-core | |||||||||
![]() | LYASE / Artificial enzyme | |||||||||
Function / homology | PHOSPHATE ION![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Kemp Eliminase 1A53-core in unbound state Authors: Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.9 KB | Display | ![]() |
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PDB format | ![]() | 128.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1008.7 KB | Display | ![]() |
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Full document | ![]() | 1008.7 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fmeC ![]() 6nw4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 29928.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.212837 Å3/Da / Density % sol: 44.44978 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6, 40% v/v PEG400, 5% w/v PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→52.56 Å / Num. obs: 11245 / % possible obs: 99.96 % / Redundancy: 9.47 % / Biso Wilson estimate: 35.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.044 / Rrim(I) all: 0.137 / Χ2: 0.99 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.36→2.45 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1152 / CC1/2: 0.932 / Rpim(I) all: 0.174 / Rrim(I) all: 0.551 / Χ2: 0.99 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6NW4 Resolution: 2.36→52.56 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.6466 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: 40.14 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→52.56 Å
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Refine LS restraints |
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LS refinement shell |
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