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Yorodumi- PDB-4awd: Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4awd | ||||||
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Title | Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut bacterium Bacteroides plebeius | ||||||
Components | BETA-PORPHYRANASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-porphyranase / beta-agarase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | BACTEROIDES PLEBEIUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hehemann, J.H. / Kelly, A.G. / Pudlo, N.A. / Martens, E.C. / Boraston, A.B. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2012 Title: Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Authors: Hehemann, J.H. / Kelly, A.G. / Pudlo, N.A. / Martens, E.C. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4awd.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4awd.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 4awd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4awd_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 4awd_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 4awd_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 4awd_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/4awd ftp://data.pdbj.org/pub/pdb/validation_reports/aw/4awd | HTTPS FTP |
-Related structure data
Related structure data | 4aw7C 3juuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37515.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES PLEBEIUS (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: B5CY92, beta-porphyranase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE RECOMBINAN | |
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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: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 23-25 % PEG 3350, 100 MM TRIS PH 8.5 AND 5 MM CALCIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97911 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.74 Å / Num. obs: 30374 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3JUU Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.219 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.055 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.518 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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