+Open data
-Basic information
Entry | Database: PDB / ID: 6zx4 | ||||||
---|---|---|---|---|---|---|---|
Title | Neisseria gonorrhoeae transaldolase | ||||||
Components | Transaldolase | ||||||
Keywords | TRANSFERASE / Sugar Metabolism / Post-Translational Modification | ||||||
Function / homology | Function and homology information transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å | ||||||
Authors | Sautner, V. / Rabe von Pappenheim, F. / Wensien, M. / Tittmann, K. | ||||||
Citation | Journal: Nature / Year: 2021 Title: A lysine-cysteine redox switch with an NOS bridge regulates enzyme function. Authors: Wensien, M. / von Pappenheim, F.R. / Funk, L.M. / Kloskowski, P. / Curth, U. / Diederichsen, U. / Uranga, J. / Ye, J. / Fang, P. / Pan, K.T. / Urlaub, H. / Mata, R.A. / Sautner, V. / Tittmann, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zx4.cif.gz | 292.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zx4.ent.gz | 218.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zx4_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6zx4_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 6zx4_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 6zx4_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zx4 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zx4 | HTTPS FTP |
-Related structure data
Related structure data | 6zwfC 6zwhC 6zwjC 7b0lC 7bbwC 7bbxC 3clmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37614.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria) Strain: ATCC 700825 / FA 1090 / Gene: tal, NGO1610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F6E9, transaldolase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CIT / | ||||
#3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41.51 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: PEG 8000, sodium chloride, citric acid, sodium phosphate, glycylglycine |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7293 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7293 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→30.87 Å / Num. obs: 190503 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.47 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.04 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 0.96→0.99 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 54087 / CC1/2: 0.53 / Rrim(I) all: 1.27 / % possible all: 97.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CLM Resolution: 0.96→30.87 Å / SU ML: 0.0986 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.8055 / Stereochemistry target values: GeoStd + Monomer Library
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→30.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|