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Yorodumi- PDB-1olq: The Trichoderma reesei cel12a P201C mutant, structure at 1.7 A re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1olq | |||||||||
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Title | The Trichoderma reesei cel12a P201C mutant, structure at 1.7 A resolution | |||||||||
Components | ENDO-BETA-1,4-GLUCANASE | |||||||||
Keywords | HYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | TRICHODERMA REESEI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Sandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Berglund, G.I. / Jones, T.A. / Mitchinson, C. | |||||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: The Humicola Grisea Cel12A Enzyme Structure at 1.2 A Resolution and the Impact of its Free Cysteine Residues on Thermal Stability Authors: Sandgren, M. / Gualfetti, P.J. / Paech, C. / Paech, S. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Berglund, G.I. / Jones, T.A. / Mitchinson, C. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1olq.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1olq.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 1olq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1olq_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 1olq_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 1olq_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1olq_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/1olq ftp://data.pdbj.org/pub/pdb/validation_reports/ol/1olq | HTTPS FTP |
-Related structure data
Related structure data | 1olrC 1h8vS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23479.369 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-234 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: O00095, cellulase #2: Sugar | #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | |
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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 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-24 ℃ / pH: 6 / 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: ESRF / Beamline: ID14-1 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 40983 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 42832 / % possible obs: 99.8 % / Redundancy: 4.3 % / Num. measured all: 184371 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8V Resolution: 1.7→20 Å / SU B: 4.26607 / SU ML: 0.14491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24664 / ESU R Free: 0.18176 Details: BABINET'S PRINCIPLE FOR SCALING HAS BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIO BULK SOLVENT MODELLING. PARAMETERS FOR MASK CALCULATION THE FOLLOWING REFINEMENT PARAMETERS ARE ...Details: BABINET'S PRINCIPLE FOR SCALING HAS BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIO BULK SOLVENT MODELLING. PARAMETERS FOR MASK CALCULATION THE FOLLOWING REFINEMENT PARAMETERS ARE NOT REPRESENTED IN THE ABOVE TEMPLATE FOR REFMAC
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Displacement parameters | Biso mean: 13.208 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.7 Å / Num. reflection obs: 40981 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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