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Yorodumi- PDB-3lrf: Crystal structure of beta-ketoacyl synthase from brucella melitensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lrf | ||||||
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Title | Crystal structure of beta-ketoacyl synthase from brucella melitensis | ||||||
Components | Beta-ketoacyl synthase | ||||||
Keywords | TRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / BETA-KETOACYL SYNTHASE / BRUCELLA MELITENSIS / Acyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Brucella melitensis biovar Abortus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Abendroth, J. / Edwards, T. / Staker, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Proteins / Year: 2020 Title: Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Authors: Patterson, E.I. / Nanson, J.D. / Abendroth, J. / Bryan, C. / Sankaran, B. / Myler, P.J. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lrf.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lrf.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrf ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrf | HTTPS FTP |
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-Related structure data
Related structure data | 3mqdC 3u0eC 3u0fC 4jv3C 1dd8S 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
#1: Protein | Mass: 45643.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria) Strain: 2308 / Gene: fabB, BAB1_2173 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2YQQ9, beta-ketoacyl-[acyl-carrier-protein] synthase I |
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#2: Chemical | ChemComp-NA / |
#3: 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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 52414 / Num. obs: 51415 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 18.47 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 34.19 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3853 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1dd8 modified with CCP4 program CHAINSAW Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.294 / SU ML: 0.037 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.1 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: 1.6→1.64 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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