[English] 日本語
Yorodumi- PDB-8anx: E329A Mutant Thermogutta terrifontis endoglucanase catalytic doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8anx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E329A Mutant Thermogutta terrifontis endoglucanase catalytic domain with C-linker from glycoside hydrolase family 5 (TtEnd5A-CDC-E329A) | |||||||||
Components | Endoglucanase | |||||||||
Keywords | HYDROLASE / endoglucanase / endocellulase / inactive mutant | |||||||||
Function / homology | Function and homology information glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | Thermogutta terrifontis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Hussain, N. / Mikolajek, H. / Naismith, J.H. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: To Be Published Title: TtEnd5A-CDC-E329A Authors: Hussain, N. / Mikolajek, H. / Naismith, J.H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8anx.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8anx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8anx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8anx_validation.pdf.gz | 412.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8anx_full_validation.pdf.gz | 413.2 KB | Display | |
Data in XML | 8anx_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 8anx_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/8anx ftp://data.pdbj.org/pub/pdb/validation_reports/an/8anx | HTTPS FTP |
-Related structure data
Related structure data | 8ag9S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39831.727 Da / Num. of mol.: 1 / Mutation: E329A Source method: isolated from a genetically manipulated source Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited ...Details: TtEnd5A-CDC-E329A is an inactive mutant of TtEnd5A-CD, in which glutamic acid (E329) has been mutated with alanine (329A). TtEnd5A-CDC itself a truncated variant of our previously deposited Thermogutta terrifontis endoglucanase from glycoside hydrolase family 5 (TtEnd5A). TtEnd5A-CDC-E329A is comprised of a catalytic domain and a linker at C-terminal (186-531 amino caids). Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: pEHISTEV vector Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / Variant (production host): OverExpress C43(DE3) / References: UniProt: A0A286RCT9, cellulase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M NH4Cl and 20%W/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→69.59 Å / Num. obs: 125321 / % possible obs: 96.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Χ2: 0.94 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.13→1.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.646 / Num. unique obs: 7072 / CC1/2: 0.392 / Χ2: 0.83 / % possible all: 75.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AG9 Resolution: 1.2→69.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.958 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.638 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→69.59 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|