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- PDB-5xen: Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xen | |||||||||
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Title | Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base | |||||||||
![]() | Cysteine synthase![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kezuka, Y. / Yoshida, Y. / Nonaka, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a hydrogen sulfide-producing enzyme (Fn1220) from Fusobacterium nucleatum in complex with L-serine-PLP Schiff base Authors: Kezuka, Y. / Yoshida, Y. / Nonaka, T. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2012 Title: Purification, crystallization and preliminary X-ray analysis of two hydrogen sulfide-producing enzymes from Fusobacterium nucleatum. Authors: Kezuka, Y. / Abe, N. / Yoshida, Y. / Nonaka, T. #2: Journal: MICROBIOLOGY (READING, ENGL.) / Year: 2010 Title: Production of hydrogen sulfide by two enzymes associated with biosynthesis of homocysteine and lanthionine in Fusobacterium nucleatum subsp. nucleatum ATCC 25586. Authors: Yoshida, Y. / Ito, S. / Kamo, M. / Kezuka, Y. / Tamura, H. / Kunimatsu, K. / Kato, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 33525.531 Da / Num. of mol.: 2 / Fragment: UNP residues 12-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 25586 / Gene: FN1220 / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 454 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-CA / #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 41% (v/v) PEG 600, 0.1M Hepes pH 7.5, 0.17M Calcium acetate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.94→63.5 Å / Num. obs: 51457 / % possible obs: 100 % / Redundancy: 27.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.4 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 27.7 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 16.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→63.5 Å
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Refine LS restraints |
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