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Yorodumi- PDB-5tu0: 1.9 Angstrom Resolution Crystal Structure of Maltose-Binding Peri... -
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-Basic information
Entry | Database: PDB / ID: 5tu0 | |||||||||
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Title | 1.9 Angstrom Resolution Crystal Structure of Maltose-Binding Periplasmic Protein MalE from Listeria monocytogenes in Complex with Maltose | |||||||||
Components | Lmo2125 protein | |||||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dimerization Domain / Transpeptidase Domain / Maltose-Binding Periplasmic Protein / MalE / Maltose | |||||||||
Function / homology | Function and homology information maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: To Be Published Title: 1.9 Angstrom Resolution Crystal Structure of Maltose-Binding Periplasmic Protein MalE from Listeria monocytogenes in Complex with Maltose. Authors: Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tu0.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tu0.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/5tu0 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/5tu0 | HTTPS FTP |
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-Related structure data
Related structure data | 2xd3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43070.801 Da / Num. of mol.: 1 / Fragment: UNP residues 33-419 / Mutation: M388K, Q400P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo2125 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q929P4 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-TTN / |
#4: Chemical | ChemComp-PGE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Protein: 15.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 2mM MAL; Screen: Classics II (C2), 1.1M Ammonium tartrate (pH 7.0). PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 33694 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.826 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XD3 Resolution: 1.9→29.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.852 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.132 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.167 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.67 Å
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Refine LS restraints |
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