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Yorodumi- PDB-7lst: Ruminococcus bromii Amy12-D392A with 63-a-D-glucosyl-maltotriosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lst | ||||||
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Title | Ruminococcus bromii Amy12-D392A with 63-a-D-glucosyl-maltotriosyl-maltotriose | ||||||
Components | Pullulanase | ||||||
Keywords | HYDROLASE / GH13 / pullulanase / CBM48 / complex | ||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Ruminococcus bromii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Koropatkin, N.M. / Cockburn, D.W. / Brown, H.A. / Kibler, R.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases. Authors: Cockburn, D.W. / Kibler, R. / Brown, H.A. / Duvall, R. / Morais, S. / Bayer, E. / Koropatkin, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lst.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lst.ent.gz | 269.4 KB | Display | PDB format |
PDBx/mmJSON format | 7lst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/7lst ftp://data.pdbj.org/pub/pdb/validation_reports/ls/7lst | HTTPS FTP |
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-Related structure data
Related structure data | 7lsaSC 7lsrC 7lsuC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 87458.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus bromii (bacteria) / Gene: pulA_2, RBL236_00821 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A2N0UU23, pullulanase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose |
-Non-polymers , 5 types, 617 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.22 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8.75 - 8.9 mg/ml of protein and 10 mM 63-a-D-glucosyl-maltotriosyl-maltotriose via hanging drop against a well solution containing 16% PEG 3350, 4% glycerol, 0.3 ammonium acetate, and 0.1 M Bis-Tris pH 6.5. |
-Data collection
Diffraction | Mean temperature: 120 K / Ambient temp details: crogenic / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2016 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→85.3 Å / Num. obs: 49996 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.99 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Num. unique obs: 4926 / CC1/2: 0.64 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LSA Resolution: 2.05→85.26 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.488 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 51.32 Å2 / Biso mean: 23.062 Å2 / Biso min: 10.34 Å2
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Refinement step | Cycle: final / Resolution: 2.05→85.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 62.3055 Å / Origin y: 101.3478 Å / Origin z: 188.202 Å
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