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Yorodumi- PDB-6nio: Crystal Structure of the Molybdate Transporter Periplasmic Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nio | ||||||
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Title | Crystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis | ||||||
Components | Molybdate ABC transporter substrate-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic Protein ModA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ACETIC ACID / FORMIC ACID / : Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å | ||||||
Authors | Kim, Y. / Joachimiak, G. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis Authors: Kim, Y. / Joachimiak, G. / Maltseva, N. / Endres, M. / Joachimiak, A. / 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 | 6nio.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nio.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 6nio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nio ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nio | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 25714.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: modA, modA2, YP_1015, C6P89_14820, NCTC144_03853 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S9PEQ7 |
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#2: Chemical | ChemComp-NHE / |
#3: Chemical | ChemComp-ACY / |
#4: Chemical | ChemComp-FMT / |
#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: 1.93 Å3/Da / Density % sol: 36.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 1.0 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→50 Å / Num. obs: 41969 / % possible obs: 99.8 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 2078 / CC1/2: 0.883 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.37→41.657 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→41.657 Å
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Refine LS restraints |
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LS refinement shell |
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