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Yorodumi- PDB-6a6g: Crystal structure of thermostable FiSufS-SufU complex from thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6g | |||||||||
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Title | Crystal structure of thermostable FiSufS-SufU complex from thermophilic Fervidobacterium Islandicum AW-1 | |||||||||
Components |
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Keywords | TRANSFERASE / Cysteine desulfurase (FiSufS) / Acceptor protein (FiSufE) / Thermophile / Suf gene cluster | |||||||||
Function / homology | Function and homology information cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / iron-sulfur cluster binding / pyridoxal phosphate binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Fervidobacterium islandicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Dhanasingh, I. / Jin, H.S. / Lee, D.W. / Lee, S.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Microb Biotechnol / Year: 2020 Title: The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation. Authors: Jin, H.S. / Dhanasingh, I. / Sung, J.Y. / La, J.W. / Lee, Y. / Lee, E.M. / Kang, Y. / Lee, D.Y. / Lee, S.H. / Lee, D.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a6g.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a6g.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a6g_validation.pdf.gz | 498.3 KB | Display | wwPDB validaton report |
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Full document | 6a6g_full_validation.pdf.gz | 509.6 KB | Display | |
Data in XML | 6a6g_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 6a6g_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6g ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6g | HTTPS FTP |
-Related structure data
Related structure data | 6a6eSC 6a6fSC 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 , 2 types, 4 molecules ABCD
#1: Protein | Mass: 47644.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08315 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1B0VPZ3, cysteine desulfurase #2: Protein | Mass: 15887.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08310 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1B0VLW5 |
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-Non-polymers , 5 types, 466 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M lithium nitrate, PEG 3350, 0.1M HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979133 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979133 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 39603 / % possible obs: 98.95 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.46 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.435 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A6E and 6A6F Resolution: 2.49→29.616 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.114 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 2.011 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.12 Å2
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Refinement step | Cycle: 1 / Resolution: 2.49→29.616 Å
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Refine LS restraints |
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