+Open data
-Basic information
Entry | Database: PDB / ID: 1hcu | ||||||
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Title | alpha-1,2-mannosidase from Trichoderma reesei | ||||||
Components | ALPHA-1,2-MANNOSIDASE | ||||||
Keywords | GLYCOSYLATION / GLYCOSYL HYDROLASE | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / protein glycosylation / carbohydrate metabolic process / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | TRICHODERMA REESEI (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Van Petegem, F. / Contreras, H. / Contreras, R. / Van Beeumen, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Trichoderma Reesei Alpha-1,2-Mannosidase: Structural Basis for the Cleavage of Four Consecutive Mannose Residues Authors: Van Petegem, F. / Contreras, H. / Contreras, R. / Van Beeumen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hcu.cif.gz | 393.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hcu.ent.gz | 321 KB | Display | PDB format |
PDBx/mmJSON format | 1hcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hcu_validation.pdf.gz | 490.2 KB | Display | wwPDB validaton report |
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Full document | 1hcu_full_validation.pdf.gz | 531.7 KB | Display | |
Data in XML | 1hcu_validation.xml.gz | 81.3 KB | Display | |
Data in CIF | 1hcu_validation.cif.gz | 116 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/1hcu ftp://data.pdbj.org/pub/pdb/validation_reports/hc/1hcu | HTTPS FTP |
-Related structure data
Related structure data | 1dl2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 54359.609 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: PICHIA PASTORIS (fungus) References: UniProt: Q9P8T8, mannosyl-oligosaccharide 1,2-alpha-mannosidase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-CA / #4: 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: 2.102 Å3/Da / Density % sol: 39.22 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4 Details: 10MG/ML PROTEIN IN 0.1M TRIS-CL PH 7.5 MIX 2 MICROLITER OF PROTEIN SOLUTION WITH 2 MICROLITER OF WELL SOLUTION IN A HANGING DROP EXPERIMENT. THE WELL CONTAINS 0.1M NA-ACETATE PH 4.0, 12% PEG 35000, 0.3M CACL2 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→20 Å / Num. obs: 73996 / % possible obs: 98.9 % / Redundancy: 4.94 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.01 |
Reflection shell | Resolution: 2.37→2.45 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 4.915 / % possible all: 95.1 |
Reflection | *PLUS Num. measured all: 818429 |
Reflection shell | *PLUS % possible obs: 95.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DL2 Resolution: 2.37→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.35 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.37→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.52 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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