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- PDB-2gbb: Crystal structure of secreted chorismate mutase from Yersinia pestis -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gbb | ||||||
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Title | Crystal structure of secreted chorismate mutase from Yersinia pestis | ||||||
![]() | putative chorismate mutase | ||||||
![]() | ISOMERASE / alpha helical bundle | ||||||
Function / homology | ![]() salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ladner, J.E. / Reddy, P.T. / Nelson, B.C. / Robinson, H. / Kim, S.-K. | ||||||
![]() | ![]() Title: A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H(37)R(v) and the secreted chorismate mutase (y2828) from Yersinia pestis. Authors: Kim, S.K. / Reddy, S.K. / Nelson, B.C. / Robinson, H. / Reddy, P.T. / Ladner, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 114.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.4 KB | Display | ![]() |
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Full document | ![]() | 507.7 KB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer. The asymmetric unit contains two dimers. |
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Components
#1: Protein | Mass: 17713.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Yersinia pestis / Strain: KIM / Gene: y2828 / Plasmid: DE3, GroEL:YpCM fusion plasmid / Production host: ![]() ![]() References: GenBank: 45435929, UniProt: Q7CHH5*PLUS, chorismate mutase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Well solution: 1.5-1.6 M ammonium sulfate, 0.1 M citrate/phosphate buffer pH 4.2. Protein solution: 5 mg/ml in 0.025 M Tris ph 7.5, 0.0005 M EDTA, 0.0005 M DTT, 0.1 M sodium chloride. Drops: ...Details: Well solution: 1.5-1.6 M ammonium sulfate, 0.1 M citrate/phosphate buffer pH 4.2. Protein solution: 5 mg/ml in 0.025 M Tris ph 7.5, 0.0005 M EDTA, 0.0005 M DTT, 0.1 M sodium chloride. Drops: 1:1 well:protein., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 13 % / Av σ(I) over netI: 8.2 / Number: 566822 / Rmerge(I) obs: 0.113 / Χ2: 1.99 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 43510 / % possible obs: 99.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 2.1→50 Å / Num. obs: 43510 / % possible obs: 99.4 % / Redundancy: 13 % / Rmerge(I) obs: 0.113 / Χ2: 1.991 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing dm | FOM : 0.67 / FOM acentric: 0.68 / FOM centric: 0.57 / Reflection: 22704 / Reflection acentric: 20607 / Reflection centric: 2097 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.383 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.216 Å / Total num. of bins used: 10
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