+Open data
-Basic information
Entry | Database: PDB / ID: 1ks5 | ||||||
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Title | Structure of Aspergillus niger endoglucanase | ||||||
Components | Endoglucanase A | ||||||
Keywords | HYDROLASE / Aspergillus niger / Endoglucanase / Cellulase / Jelly-roll / familly 12 / glycosyl hydrolase | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / polysaccharide catabolic process / transferase activity Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Khademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, C. / Meyer, E.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride. Authors: Khademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, K. / Meyer, E.F. | ||||||
History |
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Remark 650 | HELIX AUTHOR PROVIDED HELIX RECORDS | ||||||
Remark 700 | SHEET AUTHOR PROVIDED SHEET RECORDS |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ks5.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ks5.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ks5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ks5_validation.pdf.gz | 389.4 KB | Display | wwPDB validaton report |
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Full document | 1ks5_full_validation.pdf.gz | 391.6 KB | Display | |
Data in XML | 1ks5_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1ks5_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ks5 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ks5 | HTTPS FTP |
-Related 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: 24283.145 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: CBS 554.65 / References: UniProt: O74705, cellulase |
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#2: 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: 3.19 Å3/Da / Density % sol: 61.45 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG 4000, Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030K / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: mirrors |
Radiation | Monochromator: osmic, Model 140-000023 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 18707 / Num. obs: 18194 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.3 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 18660 / % possible obs: 98 % / Num. measured all: 325097 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.016
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.196 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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