+Open data
-Basic information
Entry | Database: PDB / ID: 7b0l | ||||||
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Title | Neisseria gonorrhoeae transaldolase, low-dose inhouse | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0l.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0l.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 7b0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b0l_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 7b0l_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 7b0l_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 7b0l_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0l ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0l | HTTPS FTP |
-Related structure data
Related structure data | 6zwfC 6zwhC 6zwjC 6zx4C 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-CIT / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Sodium citrate, Sodium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 9, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→44.77 Å / Num. obs: 37104 / % possible obs: 96.2 % / Redundancy: 7.266 % / Biso Wilson estimate: 21.546 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.092 / Χ2: 0.915 / Net I/σ(I): 15.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CLM Resolution: 1.65→38.14 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.91 / Stereochemistry target values: ML
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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 max: 58.86 Å2 / Biso mean: 15.4932 Å2 / Biso min: 6.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→38.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: -13.3152 Å / Origin y: 17.0347 Å / Origin z: -17.6497 Å
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Refinement TLS group |
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