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Yorodumi- PDB-4kms: Crystal structure of Acetoacetyl-CoA reductase from Rickettsia felis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kms | ||||||
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Title | Crystal structure of Acetoacetyl-CoA reductase from Rickettsia felis | ||||||
Components | Acetoacetyl-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Rickettsia felis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lukacs, C. / Edwards, T.E. / Lorimer, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. Authors: Rodarte, J.V. / Abendroth, J. / Edwards, T.E. / Lorimer, D.D. / Staker, B.L. / Zhang, S. / Myler, P.J. / McLaughlin, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kms.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kms.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/4kms ftp://data.pdbj.org/pub/pdb/validation_reports/km/4kms | HTTPS FTP |
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-Related structure data
Related structure data | 7mi0C 3ezlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: -2 - 238 / Label seq-ID: 6 - 246
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-Components
#1: Protein | Mass: 27312.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia felis (bacteria) / Strain: ATCC VR-1525 / URRWXCal2 / Gene: phbB, RF_015, RF_0153 / Plasmid: RifeA.00170.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4UN54, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23 mg/mL RifeA.00170.a.B1.PS01660, MCSG1 screen condition G1: 10% PEG8000, 8% ethylene glycol, 100 mM HEPES/NaOH, pH 7.5, Tray 241460g1, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2012 / Details: Rh coated flat mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. all: 38963 / Num. obs: 38871 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.83 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.78 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EZL Resolution: 2→46.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.49 / SU ML: 0.093 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 89.31 Å2 / Biso mean: 39.9812 Å2 / Biso min: 19.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13137 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.052 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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