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Yorodumi- PDB-4bkr: Enoyl-ACP reductase from Yersinia pestis (wildtype, removed Hista... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bkr | ||||||
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Title | Enoyl-ACP reductase from Yersinia pestis (wildtype, removed Histag) with cofactor NADH | ||||||
Components | PUTATIVE REDUCTASE YPZ3_3519 | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / ENOYL-ACP REDUCTASE | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / : Function and homology information | ||||||
Biological species | YERSINIA PESTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Hirschbeck, M.W. / Neckles, C. / Tonge, P.J. / 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 | 4bkr.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bkr.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bkr ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bkr | HTTPS FTP |
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-Related structure data
Related structure data | 4bkqC 5g2oC 5jaiC 5jamC 5jaqC 3zu3S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44203.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Strain: A1122 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: G0JFF6, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 5 types, 510 molecules
#2: Chemical | ChemComp-NAI / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | NCBI REFERENCE SEQUENCE FOR THIS SEQUENCE IS NP_671410.1 |
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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: 2.92 Å3/Da / Density % sol: 57.89 % / Description: NONE |
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Crystal grow | 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: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.58 Å / Num. obs: 48371 / % possible obs: 100 % / Observed criterion σ(I): 4.9 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZU3 Resolution: 1.798→33.58 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.04 / 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 / Bsol: 36.622 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.798→33.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 36.9306 Å / Origin y: -13.1815 Å / Origin z: 6.203 Å
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Refinement TLS group | Selection details: (CHAIN A AND RESSEQ -10:9999) |