+Open data
-Basic information
Entry | Database: PDB / ID: 1ukr | ||||||
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Title | STRUCTURE OF ENDO-1,4-BETA-XYLANASE C | ||||||
Components | ENDO-1,4-B-XYLANASE I | ||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE | ||||||
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 | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Krengel, U. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum. Authors: Krengel, U. / Dijkstra, B.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary Crystallographic Analysis of Endo-1,4-Beta-Xyalanase I from Aspergillus Niger Authors: Krengel, U. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ukr.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ukr.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ukr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ukr_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1ukr_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 1ukr_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 1ukr_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1ukr ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1ukr | HTTPS FTP |
-Related structure data
Related structure data | 1xndS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19855.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P55329, endo-1,4-beta-xylanase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % | |||||||||||||||
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Crystal grow | Method: vapor diffusion - sitting drop - macroseeding / pH: 4.7 Details: SITTING DROP SETUP USING SILICONIZED GLASS WELLS USING 15 MICROLITER DROPS AT ROOM TEMPERATURE AND MACROSEEDING. PROTEIN SOLUTION: 4.5 MG/ML IN 10 MM NA ACETATE PH 4.7. RESERVOIR SOLUTION: 1. ...Details: SITTING DROP SETUP USING SILICONIZED GLASS WELLS USING 15 MICROLITER DROPS AT ROOM TEMPERATURE AND MACROSEEDING. PROTEIN SOLUTION: 4.5 MG/ML IN 10 MM NA ACETATE PH 4.7. RESERVOIR SOLUTION: 1.5 ML 1.8 M NA2S2O3 (PH 8.0)., vapor diffusion - sitting drop - macroseeding Temp details: room temp | |||||||||||||||
Crystal grow | *PLUS Temperature: 295, 277, 310 K / Method: vapor diffusion, hanging drop / Details: or sitting drop vapor diffusion or batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.06 Å / Num. obs: 33131 / % possible obs: 95.3 % / Redundancy: 4.6 % / Rsym value: 0.082 |
Reflection | *PLUS Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TRICHODERMA HARZIANUM XYLANASE, PDB ENTRY 1XND. Resolution: 2.4→6 Å / σ(F): 0 Details: REFINEMENT INCLUDED NCS-RESTRAINTS AT PLACES WITHOUT CRYSTAL CONTACTS. ONLY IN THE FINAL REFINEMENT CYCLE ALL DATA WERE INCLUDED. IN THE EARLIER STAGES OF REFINEMENT, 10% OF THE DATA WERE ...Details: REFINEMENT INCLUDED NCS-RESTRAINTS AT PLACES WITHOUT CRYSTAL CONTACTS. ONLY IN THE FINAL REFINEMENT CYCLE ALL DATA WERE INCLUDED. IN THE EARLIER STAGES OF REFINEMENT, 10% OF THE DATA WERE TAKEN TO CALCULATE A FREE R-FACTOR (R=17.7 AND RFREE=21.9 %, RESPECTIVELY).
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Displacement parameters | Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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