+Open data
-Basic information
Entry | Database: PDB / ID: 4bf7 | ||||||
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Title | Emericilla nidulans endo-beta-1,4-galactanase | ||||||
Components | ARABINOGALACTAN ENDO-1,4-BETA-GALACTOSIDASE A | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / cell wall organization / extracellular region Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Otten, H. / Michalak, M. / Larsen, S. / Mikkelsen, J.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: The Binding of Zinc Ions to Emericella Nidulans Endo-[Beta]-1,4-Galactanase is Essential for Crystal Formation Authors: Otten, H. / Michalak, M. / Mikkelsen, J.D. / Larsen, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bf7.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bf7.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bf7_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 4bf7_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 4bf7_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4bf7_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bf7 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bf7 | HTTPS FTP |
-Related structure data
Related structure data | 1fobS 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 38736.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SULFIDE BRIDGES BETWEEN A C253-C310 Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Production host: KOMAGATAELLA PASTORIS (fungus) References: UniProt: Q5B153, arabinogalactan endo-beta-1,4-galactanase |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 209 molecules
#2: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | FUNGAL GENETICS STOCK CENTER |
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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: 3 Å3/Da / Density % sol: 59.5 % / Description: NONE |
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Crystal grow | pH: 8 Details: 200 MM ZN ACETATE, 100 MM IMIDAZOLE, 20%(W/V) PEG 3000, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2012 Details: ONE PAIR OF PT COATED SI FOCUSING MIRRORS, KIRKPATRICK-BAEZ GEOMETRY |
Radiation | Monochromator: HORIZONTALLY DIFFRACTING SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→47 Å / Num. obs: 58261 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FOB Resolution: 2.001→47.475 Å / SU ML: 0.18 / σ(F): 1.21 / Phase error: 17.04 / Stereochemistry target values: ML Details: N-TERMINAL 1-17 MILSSLLPLSLVTLTSA IS DISORDERED AND NOT MODELLED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→47.475 Å
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Refine LS restraints |
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LS refinement shell |
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