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- PDB-4l27: Crystal structure of delta1-39 and delta516-525 human cystathioni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l27 | ||||||
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Title | Crystal structure of delta1-39 and delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag | ||||||
![]() | Cystathionine beta-synthase | ||||||
![]() | LYASE / CBS domain / homocyteine / cysteine biosynthesis / heme / pyridoxal 5'-phosphate / S-adenosylmethionine / transsulfuration pathway | ||||||
Function / homology | ![]() Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cystathionine beta-synthase activity ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cystathionine beta-synthase activity / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / regulation of nitric oxide mediated signal transduction / cysteine biosynthetic process / L-cysteine catabolic process / cerebellum morphogenesis / cysteine synthase activity / L-cysteine desulfhydrase activity / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / L-serine catabolic process / endochondral ossification / transsulfuration / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / blood vessel remodeling / maternal process involved in female pregnancy / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ereno, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez, L.A. | ||||||
![]() | ![]() Title: Structural basis of regulation and oligomerization of human cystathionine beta-synthase, the central enzyme of transsulfuration. Authors: Ereno-Orbea, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez-Cruz, L.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 389.2 KB | Display | ![]() |
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PDB format | ![]() | 318.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 74.2 KB | Display | |
Data in CIF | ![]() | 95.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l0dC ![]() 4l28C ![]() 4l3vC ![]() 4lod C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60513.188 Da / Num. of mol.: 4 / Mutation: D444N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-HEM / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M ammonium citrate tribasic, 0.1 M imidazole, 20% w/v PEG2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.391→57 Å / Num. all: 40186 / Num. obs: 40186 / % possible obs: 99.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.61 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.71 |
Reflection shell | Resolution: 3.391→3.51 Å / Redundancy: 8.27 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.99 / % possible all: 97.25 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LOD ![]() 4lod Resolution: 3.391→56.622 Å / SU ML: 0.47 / σ(F): 2 / Phase error: 26.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.391→56.622 Å
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Refine LS restraints |
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LS refinement shell |
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