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Yorodumi- PDB-4nzf: Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nzf | ||||||
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Title | Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus), in complex with arabinose | ||||||
Components | Abp, a GH27 beta-L-arabinopyranosidase | ||||||
Keywords | HYDROLASE / Tim Barrel / Glycoside Hydrolase | ||||||
Function / homology | Function and homology information Golgi alpha-mannosidase II / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Lansky, S. / Solomon, H.V. / Salama, R. / Belrhali, H. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure-specificity relationships in Abp, a GH27 beta-L-arabinopyranosidase from Geobacillus stearothermophilus T6 Authors: Lansky, S. / Salama, R. / Solomon, H.V. / Feinberg, H. / Belrhali, H. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nzf.cif.gz | 756.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nzf.ent.gz | 627.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzf ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzf | HTTPS FTP |
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-Related structure data
Related structure data | 4nx0C 4nxkSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 16 molecules ABCDEFGH
#1: Protein | Mass: 51197.164 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) #3: Sugar | ChemComp-ARB / |
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-Non-polymers , 4 types, 3040 molecules
#2: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CIT / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE UNP SEQUENCE DATABASE REFERENCES |
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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: 3.8 Å3/Da / Density % sol: 67.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.8M Ammonium Sulfate, 0.1M citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2013 |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→34.71 Å / Num. all: 301393 / Num. obs: 268240 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.19→2.25 Å / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NXK Resolution: 2.19→34.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.544 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→34.71 Å
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Refine LS restraints |
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