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Yorodumi- PDB-4coo: Crystal structure of human cystathionine beta-synthase (delta516-... -
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-Basic information
Entry | Database: PDB / ID: 4coo | ||||||
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Title | Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution | ||||||
Components | CYSTATHIONINE BETA-SYNTHASE | ||||||
Keywords | LYASE / METHIONINE CYCLE / METABOLIC PATHWAY / ALLOSTERIC REGULATION / SERINE METABOLISM | ||||||
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 / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / 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 / L-serine catabolic process / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / 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: 2 Å | ||||||
Authors | McCorvie, T.J. / Kopec, J. / Vollamar, M. / Strain-Damerell, C. / Bushell, S. / Bradley, A. / Tallant, C. / Kiyani, W. / Froese, D.S. / Carpenter, E.S. ...McCorvie, T.J. / Kopec, J. / Vollamar, M. / Strain-Damerell, C. / Bushell, S. / Bradley, A. / Tallant, C. / Kiyani, W. / Froese, D.S. / Carpenter, E.S. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Inter-Domain Communication of Human Cystathionine Beta Synthase: Structural Basis of S-Adenosyl-L-Methionine Activation. Authors: Mccorvie, T.J. / Kopec, J. / Hyung, S. / Fitzpatrick, F. / Feng, X. / Termine, D. / Strain-Damerell, C. / Vollmar, M. / Fleming, J. / Janz, J.M. / Bulawa, C. / Yue, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4coo.cif.gz | 403.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4coo.ent.gz | 328.2 KB | Display | PDB format |
PDBx/mmJSON format | 4coo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4coo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4coo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4coo_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 4coo_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4coo ftp://data.pdbj.org/pub/pdb/validation_reports/co/4coo | HTTPS FTP |
-Related structure data
Related structure data | 4uuuC 1jbqS 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, 2 molecules AB
#1: Protein | Mass: 62132.949 Da / Num. of mol.: 2 Fragment: CATALYTIC AND REGULATORY DOMAINS, RESIDUES 1-515,526-551 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P35520, cystathionine beta-synthase |
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-Non-polymers , 7 types, 313 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PE4 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT USED HERE CONTAINS A DELETION OF AMINO ACIDS 516-525 |
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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: 2.89 Å3/Da / Density % sol: 57.42 % / Description: NONE |
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Crystal grow | Details: 18% PEG8000, 0.1 M CACODYLATE, PH 6.6 0.2 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.89 Å / Num. obs: 93295 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JBQ Resolution: 2→95.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.023 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / 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: 43.704 Å2
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Refinement step | Cycle: LAST / Resolution: 2→95.56 Å
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