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Yorodumi- PDB-4jv3: Crystal structure of beta-ketoacyl synthase from Brucella meliten... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jv3 | ||||||
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Title | Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin | ||||||
Components | Beta-ketoacyl synthase | ||||||
Keywords | Transferase/Antibiotic / SSGCID / beta-ketoacyl synthase / platencin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Brucella melitensis biovar Abortus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | 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 | 4jv3.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jv3.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 4jv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jv3_validation.pdf.gz | 751.5 KB | Display | wwPDB validaton report |
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Full document | 4jv3_full_validation.pdf.gz | 752.2 KB | Display | |
Data in XML | 4jv3_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4jv3_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/4jv3 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/4jv3 | HTTPS FTP |
-Related structure data
Related structure data | 3lrfSC 3mqdC 3u0eC 3u0fC 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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Details | biological unit is a dimer generated from the monomer in the asymmetric unit by the operation: -X+1, Y, -Z+1 |
-Components
#1: Protein | Mass: 45723.336 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-N32 / |
#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: 2.3 Å3/Da / Density % sol: 46.41 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MD PACT screen, H2: 20% PEG 3350, 100mM BisTrisPropane pH 8.5, 200mM Na-bromide; tray 233841 f11, BrabA.00113.a at 23 mg/ml, 2.5mM platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 7, 2013 / Details: Rigaku VariMax | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 45545 / Num. obs: 44869 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 20.929 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 47.79 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3LRF Resolution: 1.7→42.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.159 / WRfactor Rwork: 0.1335 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9088 / SU B: 2.772 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0868 / SU Rfree: 0.0843 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.084 / 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: 49.4 Å2 / Biso mean: 16.929 Å2 / Biso min: 3.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→42.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 25.63 Å / Origin y: 2.007 Å / Origin z: 17.864 Å
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