+Open data
-Basic information
Entry | Database: PDB / ID: 3akp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of xylanase from Trichoderma longibrachiatum | |||||||||
Components | xylanase | |||||||||
Keywords | HYDROLASE / xylanase | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | Trichoderma longibrachiatum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å | |||||||||
Authors | Sugahara, M. / Kunishima, N. | |||||||||
Citation | Journal: Cryst.Growth Des. / Year: 2011 Title: Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite as a Heteroepitaxic Nucleant Authors: Sugahara, M. / Kageyama-Morikawa, Y. / Kunishima, N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3akp.cif.gz | 92 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3akp.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 3akp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3akp ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3akp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20838.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoderma longibrachiatum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: F8W669*PLUS, endo-1,4-beta-xylanase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THERE IS NO DATABASE REFERENCE SEQUENCE AT PROCESSING | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: oil microbatch / pH: 8.5 Details: 30% PEG 4000, 0.2M sodium acetate, pH 8.5, oil microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jan 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40 Å / Num. all: 105854 / Num. obs: 105854 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.076 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3 / Num. unique all: 9839 / Rsym value: 0.442 / % possible all: 89.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.2→22.83 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→22.83 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.2→1.24 Å / Rfactor Rfree error: 0.013
|