+Open data
-Basic information
Entry | Database: PDB / ID: 6w3z | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS) | ||||||||||||
Components | BMA-DHPS-1, isoform a | ||||||||||||
Keywords | TRANSFERASE / Brugia malayi / Deoxyhypusine synthase / Structural Genomics Consortium / SGC | ||||||||||||
Function / homology | peptidyl-lysine modification to peptidyl-hypusine / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / BMA-DHPS-1, isoform a Function and homology information | ||||||||||||
Biological species | Brugia malayi (agent of lymphatic filariasis) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||||||||
Authors | Santiago, A.S. / dos Reis, C.V. / Ramos, P.Z. / Klippel, H.A. / Silva, S.F. / Zanelli, C.F. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | Brazil, 3items
| ||||||||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2020 Title: Structural features and development of an assay platform of the parasite target deoxyhypusine synthase of Brugia malayi and Leishmania major. Authors: Silva, S.F. / Klippel, A.H. / Ramos, P.Z. / Santiago, A.D.S. / Valentini, S.R. / Bengtson, M.H. / Massirer, K.B. / Bilsland, E. / Counago, R.M. / Zanelli, C.F. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6w3z.cif.gz | 283 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6w3z.ent.gz | 225.4 KB | Display | PDB format |
PDBx/mmJSON format | 6w3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w3z_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6w3z_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6w3z_validation.xml.gz | 52 KB | Display | |
Data in CIF | 6w3z_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/6w3z ftp://data.pdbj.org/pub/pdb/validation_reports/w3/6w3z | HTTPS FTP |
-Related structure data
Related structure data | 1rqdS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41131.301 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis) Gene: bma-dhps-1, Bm1_16300, Bma-dhps-1, Bm14681, BM_Bm14681 Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3 / References: UniProt: A0A0J9XTC4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 0.2M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018 Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96858 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→29.42 Å / Num. obs: 62547 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.084 / Rrim(I) all: 0.155 / Net I/σ(I): 5.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQD Resolution: 2.3→29.41 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.379 / SU ML: 0.21 / SU R Cruickshank DPI: 0.3769 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.218 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.5 Å2 / Biso mean: 34.024 Å2 / Biso min: 17.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→29.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|