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Open data
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Basic information
Entry | Database: PDB / ID: 3m7t | ||||||
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Title | Crystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant | ||||||
![]() | Alpha-lytic protease | ||||||
![]() | HYDROLASE / Disulfide bond / Protease / Serine protease / Zymogen | ||||||
Function / homology | ![]() alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agard, D.A. / Erciyas Bailey, F.P. / Waddling, C.A. | ||||||
![]() | ![]() Title: Quantifying protein unfolding cooperativity with acid sensitive probes: Interdomain salt bridge contributions to unfolding cooperativity are combined efficiently in alpha-Lytic Protease Authors: Erciyas Bailey, F.P. / Waddling, C.A. / Agard, D.A. #1: ![]() Title: The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain. Authors: Fuhrmann, C.N. / Kelch, B.A. / Ota, N. / Agard, D.A. #2: ![]() Title: Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution. Authors: Rader, S.D. / Agard, D.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 | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m7uC ![]() 1ssxS C: citing same article ( S: Starting model for refinement |
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Similar 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
#1: Protein | Mass: 19746.979 Da / Num. of mol.: 1 / Fragment: MATURE PROTEASE DOMAIN (RESIDUES 1-198) / Mutation: E8A, R105S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.3 M lithium sulfate, 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2009 / Details: Double Crystal Si(111) |
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→57.171 Å / Num. all: 29718 / Num. obs: 29042 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 36.575 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.676 / Num. unique all: 1461 / Rsym value: 0.457 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1SSX Resolution: 1.55→33.008 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: TWIN_LSQ_F Details: protein atoms refined anisotropically, water atoms refined isotropically
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.419 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.55→33.008 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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