+Open data
-Basic information
Entry | Database: PDB / ID: 7qsj | ||||||
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Title | Methylmannose polysaccharide hydrolase MmpH from M. hassiacum | ||||||
Components | Methylmannose polysaccharide hydrolase (MmpH) | ||||||
Keywords | HYDROLASE / Methylmannose polysaccharide / Mycobacterium hassiacum / endomannosidase | ||||||
Function / homology | Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / NICKEL (II) ION / Prenyltransferase Function and homology information | ||||||
Biological species | Mycolicibacterium hassiacum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Ripoll-Rozada, J. / Manso, J.A. / Pereira, P.J.B. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Authors: Maranha, A. / Costa, M. / Ripoll-Rozada, J. / Manso, J.A. / Miranda, V. / Mendes, V.M. / Manadas, B. / Macedo-Ribeiro, S. / Ventura, M.R. / Pereira, P.J.B. / Empadinhas, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qsj.cif.gz | 375.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qsj.ent.gz | 253.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qsj_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 7qsj_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 7qsj_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 7qsj_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/7qsj ftp://data.pdbj.org/pub/pdb/validation_reports/qs/7qsj | HTTPS FTP |
-Related structure data
Related structure data | 7qsgC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41240.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: MHAS_04404 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3P4A4D3 #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 0.02 M MgCl2, 21% (w/v) polyacrylic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9809 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→49.51 Å / Num. obs: 156986 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0237 / Rpim(I) all: 0.0237 / Rrim(I) all: 0.03352 / Net I/σ(I): 16.42 |
Reflection shell | Resolution: 1.35→1.398 Å / Rmerge(I) obs: 0.6802 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 15681 / CC1/2: 0.537 / Rpim(I) all: 0.6802 / Rrim(I) all: 0.9619 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→49.51 Å / SU ML: 0.1824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5689 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→49.51 Å
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Refine LS restraints |
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LS refinement shell |
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