+Open data
-Basic information
Entry | Database: PDB / ID: 1bg4 | |||||||||
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Title | XYLANASE FROM PENICILLIUM SIMPLICISSIMUM | |||||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | |||||||||
Keywords | FAMILY 10 XYLANASE / PENICILLIUM SIMPLICISSIMUM / TIM-BARREL / GLYCOSYL HYDROLASE | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Penicillium simplicissimum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Schmidt, A. / Kratky, C. | |||||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Structure of the xylanase from Penicillium simplicissimum. Authors: Schmidt, A. / Schlacher, A. / Steiner, W. / Schwab, H. / Kratky, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bg4.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bg4.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bg4 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bg4 | HTTPS FTP |
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-Related structure data
Related structure data | 1xyzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32566.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PENICILLIUM SIMPLICISSIMUM (OUDEM.) THOM / Source: (natural) Penicillium simplicissimum (fungus) / Cellular location: SECRETEDSecretion / References: UniProt: P56588, endo-1,4-beta-xylanase | ||||||
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#2: Chemical | ChemComp-NA / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62 % Description: DATA WERE COLLECTED AT THE ELETTRA SYNCHROTRON LIGHT SOURCE, TRIESTE, ITALY | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.4 Details: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.85 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1997 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→10 Å / Num. obs: 43712 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.059 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.232 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XYZ Resolution: 1.75→10 Å / Rfactor Rfree error: 0.0034 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R THROUGHOUT / σ(F): 0 Details: PARAMETER/TOPOLOGY FILES FOR HET GROUPS EXCEPT WATER SELF-SETUP
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Displacement parameters | Biso mean: 10 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.268 |