+Open data
-Basic information
Entry | Database: PDB / ID: 6zwf | ||||||
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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: 1.05 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 | 6zwf.cif.gz | 305.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zwf.ent.gz | 244.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zwf_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 6zwf_full_validation.pdf.gz | 458.2 KB | Display | |
Data in XML | 6zwf_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6zwf_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/6zwf ftp://data.pdbj.org/pub/pdb/validation_reports/zw/6zwf | HTTPS FTP |
-Related structure data
Related structure data | 6zwhC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37598.688 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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-Non-polymers , 5 types, 482 molecules
#2: Chemical | ChemComp-EDO / | ||||
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#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | ChemComp-BME / #5: Chemical | ChemComp-OXY / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-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: 40.74 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: PEG8000, Citrate, Sodium phosphate, Sodium chloride, Glycylglycin |
-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: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7293 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→41.455 Å / Num. obs: 145716 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 11.22 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.074 / Net I/σ(I): 10.91 |
Reflection shell | Resolution: 1.05→1.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 18762 / CC1/2: 0.506 / Rrim(I) all: 1.98 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CLM Resolution: 1.05→41.455 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.33 Å2 / Biso mean: 16.1688 Å2 / Biso min: 7.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.05→41.455 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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