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Yorodumi- PDB-4l3v: Crystal structure of delta516-525 human cystathionine beta-synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l3v | ||||||
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Title | Crystal structure of delta516-525 human cystathionine beta-synthase | ||||||
Components | Cystathionine beta-synthase | ||||||
Keywords | LYASE / CBS domain / homocyteine / cysteine biosynthesis / heme / pyridoxal 5'-phosphate / S-adenosylmethionine / transsulfuration pathway | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.628 Å | ||||||
Authors | Ereno, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez, L.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l3v.cif.gz | 297.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l3v.ent.gz | 241.5 KB | Display | PDB format |
PDBx/mmJSON format | 4l3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l3v_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4l3v_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4l3v_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 4l3v_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l3v ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l3v | HTTPS FTP |
-Related structure data
Related structure data | 4l0dC 4l27C 4l28C 4lod C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60534.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: P35520, cystathionine beta-synthase #2: Chemical | #3: Chemical | |
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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: 5.76 Å3/Da / Density % sol: 78.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 30% v/v PEG550, 0.1 M sodium citrate tribasic dehydrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å |
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: 3.628→48.516 Å / Num. all: 46253 / Num. obs: 46253 / % possible obs: 96.55 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 7.25 |
Reflection shell | Resolution: 3.628→3.75 Å / Redundancy: 2.37 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 2.28 / % possible all: 72.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LOD 4lod Resolution: 3.628→48.516 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 24.54 / 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: 3.628→48.516 Å
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Refine LS restraints |
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LS refinement shell |
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