+Open data
-Basic information
Entry | Database: PDB / ID: 6zwh | ||||||
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Title | Neisseria gonorrhoeae transaldolase at 1.5 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: 1.5 Å | ||||||
Authors | Rabe von Pappenheim, F. / Wensien, M. / Funk, L.-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 | 6zwh.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zwh.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/6zwh ftp://data.pdbj.org/pub/pdb/validation_reports/zw/6zwh | HTTPS FTP |
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-Related structure data
Related structure data | 6zwfC 6zwjC 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 (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 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-ACT / |
#5: 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: 41.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: PEG8000, Ammonium acetate, Sodium chloride, Glycylglycine, DTT |
-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: 1.001 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.49 Å / Num. obs: 51609 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 16.18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.141 / Net I/σ(I): 11.33 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 1.3 % / Num. unique obs: 8931 / CC1/2: 0.785 / Rrim(I) all: 1.609 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CLM Resolution: 1.5→41.49 Å / SU ML: 0.1602 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.2537 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.49 Å
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Refine LS restraints |
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LS refinement shell |
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