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- PDB-3op4: Crystal structure of putative 3-ketoacyl-(acyl-carrier-protein) r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3op4 | ||||||
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Title | Crystal structure of putative 3-ketoacyl-(acyl-carrier-protein) reductase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with NADP+ | ||||||
![]() | 3-oxoacyl-[acyl-carrier protein] reductase | ||||||
![]() | OXIDOREDUCTASE / 3-ketoacyl-(acyl-carrier-protein) reductase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Rossmann fold / bacterial cell | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, J. / Chruszcz, M. / Onopriyenko, O. / Grimshaw, S. / Porebski, P. / Zheng, H. / Savchenko, A. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae. Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.4 KB | Display | ![]() |
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PDB format | ![]() | 148 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rroC ![]() 3rshC ![]() 3tzcC ![]() 3tzkC ![]() 3u09C ![]() 4i08C ![]() 4wjzC ![]() 4wk6C ![]() 5endC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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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: 26695.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: N16961 / Gene: VCD_002346 / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: C3NP04, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2M NH4 Sulfate,0.1M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2010 / Details: Mirror |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 61433 / Num. obs: 61433 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3009 / Rsym value: 0.616 / % possible all: 100 |
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.407 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.644 Å / Total num. of bins used: 20
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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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