+Open data
-Basic information
Entry | Database: PDB / ID: 7czc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo-FabG from Vibrio harveyi | ||||||
Components | 3-oxoacyl-ACP reductase FabG | ||||||
Keywords | OXIDOREDUCTASE / 3-oxo-acyl-ACP reductase / Rossmann fold / SDR-family / fatty acid metabolism | ||||||
Function / homology | 3-oxoacyl-(acyl-carrier-protein) reductase, putative / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / DI(HYDROXYETHYL)ETHER / 3-oxoacyl-ACP reductase FabG Function and homology information | ||||||
Biological species | Vibrio harveyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Singh, B.K. / Kumar, A. / Paul, B. / Biswas, R. / Das, A.K. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of apo-FabG from Vibrio harveyi Authors: Singh, B.K. / Kumar, A. / Paul, B. / Biswas, R. / Das, A.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7czc.cif.gz | 341.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7czc.ent.gz | 280.7 KB | Display | PDB format |
PDBx/mmJSON format | 7czc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/7czc ftp://data.pdbj.org/pub/pdb/validation_reports/cz/7czc | HTTPS FTP |
---|
-Related structure data
Related structure data | 1i01S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25978.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: AL538_14035, VCHENC02_3091 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: K5VE97 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.15M DL-malic acid (pH 7.2) , 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.7504 Å / Num. obs: 65055 / % possible obs: 99.83 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 21.02 |
Reflection shell | Resolution: 2→2.071 Å / Num. unique obs: 6451 / CC1/2: 0.858 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I01 Resolution: 2→19.749 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.98 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.66 Å2 / Biso mean: 31.6565 Å2 / Biso min: 15.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→19.749 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|