+Open data
-Basic information
Entry | Database: PDB / ID: 5g2o | |||||||||
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Title | Yersinia pestis FabV variant T276A | |||||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | |||||||||
Biological species | Yersinia pestis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Pschibul, A. / Kuper, J. / HIrschbeck, M. / Kisker, C. | |||||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia Pestis Fabv Enoyl-Acp Reductase. Authors: Neckles, C. / Pschibul, A. / Lai, C. / Hirschbeck, M. / Kuper, J. / Davoodi, S. / Zou, J. / Liu, N. / Pan, P. / Shah, S. / Daryaee, F. / Bommineni, G.R. / Lai, C. / Simmerling, C. / Kisker, C. / Tonge, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2o.cif.gz | 267.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2o.ent.gz | 222.6 KB | Display | PDB format |
PDBx/mmJSON format | 5g2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g2o_validation.pdf.gz | 778.7 KB | Display | wwPDB validaton report |
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Full document | 5g2o_full_validation.pdf.gz | 782.8 KB | Display | |
Data in XML | 5g2o_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 5g2o_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2o ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2o | HTTPS FTP |
-Related structure data
Related structure data | 4bkqC 4bkrSC 5jaiC 5jamC 5jaqC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44173.812 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: fabV, YPO4104, y4119, YP_4011 / Plasmid: PETM15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8Z9U1, enoyl-[acyl-carrier-protein] reductase (NADH) | ||
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#2: Chemical | ChemComp-NAI / | ||
#3: Chemical | #4: 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: 2.92 Å3/Da / Density % sol: 57.89 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 150 MM (NH4)2SO4 25-38% PEG 4000 100 MM MES PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91801 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.67 Å / Num. obs: 41201 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.01 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BKR Resolution: 1.9→44.668 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.668 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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