+Open data
-Basic information
Entry | Database: PDB / ID: 6zwj | ||||||
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Title | Neisseria gonorrhoeae transaldolase at 1.35 Angstrom resolution | ||||||
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: 1.35 Å | ||||||
Authors | Rabe von Pappenheim, F. / Wensien, M. / Sautner, V. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zwj.cif.gz | 253.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zwj.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zwj_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 6zwj_full_validation.pdf.gz | 435.7 KB | Display | |
Data in XML | 6zwj_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6zwj_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/6zwj ftp://data.pdbj.org/pub/pdb/validation_reports/zw/6zwj | HTTPS FTP |
-Related structure data
Related structure data | 6zwfC 6zwhC 6zx4C 7b0lC 7bbwC 7bbxC 3clmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37614.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: tal, E8M68_10680, WHOO_01512, WHOO_01712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FXY0, transaldolase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: PEG8000, Citrate, Sodium Phosphate, Sodium Chloride, Glycylglycine |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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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 12, 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: 1.35→39.73 Å / Num. obs: 67040 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.08 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6987 / CC1/2: 0.5 / Rrim(I) all: 1.21 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CLM Resolution: 1.35→39.73 Å / SU ML: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.6332 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→39.73 Å
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Refine LS restraints |
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LS refinement shell |
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