+Open data
-Basic information
Entry | Database: PDB / ID: 1b3w | ||||||||||||
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Title | XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOBIOSE | ||||||||||||
Components | PROTEIN (XYLANASE) | ||||||||||||
Keywords | FAMILY 10 XYLANASE / PENICILLIUM SIMPLICISSIMUM / GLYCOSYL HYDROLASE / SUBSTRATE BINDING | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Schmidt, A. / Kratky, C. | ||||||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant. Authors: Schmidt, A. / Gubitz, G.M. / Kratky, C. #1: 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 | 1b3w.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b3w.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b3w ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b3w | HTTPS FTP |
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-Related structure data
Related structure data | 1b30C 1b31C 1b3vC 1b3xC 1b3yC 1b3zC 1bg4S S: Starting model for refinement C: citing same article (ref.) |
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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: GenBank: AF070417, UniProt: P56588*PLUS, endo-1,4-beta-xylanase |
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#2: Polysaccharide | alpha-D-xylopyranose-(1-4)-beta-D-xylopyranose |
#3: Sugar | ChemComp-XYP / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | XYLOSE UNITS 505 AND 506 BETA-1,4 LINKED |
-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 % | ||||||||||||||||||||
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Crystal grow | pH: 8.4 Details: CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C | ||||||||||||||||||||
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: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. obs: 13208 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.108 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.36 / % possible all: 95.7 |
Reflection | *PLUS Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BG4 Resolution: 2.6→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R THROUGHOUT / σ(F): 0 Details: PARAMETER/TOPOLOGY FILES FOR HET GROUPS EXCEPT WATER SELF-SETUP
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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LS refinement shell | Resolution: 2.6→2.72 Å / 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 Rfactor obs: 0.199 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.288 |