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Yorodumi- PDB-1jbq: STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jbq | ||||||
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Title | STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN | ||||||
Components | CYSTATHIONINE BETA-SYNTHASECystathionine beta synthase | ||||||
Keywords | LYASE / Fold type II of PLP enzymes | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cartilage development involved in endochondral bone morphogenesis / L-serine metabolic process / regulation of nitric oxide mediated signal transduction / L-cysteine catabolic process / cysteine biosynthetic process / cerebellum morphogenesis / 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 / maternal process involved in female pregnancy / blood vessel remodeling / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Meier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure of human cystathionine beta-synthase: a unique pyridoxal 5'-phosphate-dependent heme protein. Authors: Meier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray diffraction analysis of the active core of human recombinant cystathionine beta-synthase: an enzyme involved in vascular disease. Authors: Janosik, M. / Meier, M. / Kery, V. / Oliveriusova, J. / Burkhard, P. / Kraus, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jbq.cif.gz | 419 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jbq.ent.gz | 341.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jbq ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jbq | HTTPS FTP |
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-Related structure data
Related structure data | 1d6sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 47520.074 Da / Num. of mol.: 6 / Fragment: THE ACTIVE CORE / Mutation: DELETION 414-551, EXTRA 23 RESIDUES AT N-TERMINUS Source method: isolated from a genetically manipulated source Details: MINOR ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-5X-1HCBSD414-551 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE MRF / References: UniProt: P35520, cystathionine beta-synthase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1000, HEPES, pH 7.5 , VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 Details: Janosik, M., (2001) Acta Crystallogr., Sect.D, 57, 289. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. all: 87368 / Num. obs: 63971 / % possible obs: 82.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 10 | ||||||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.31 / % possible all: 65.1 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.076 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 63.9 % / Rmerge(I) obs: 0.309 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D6S Resolution: 2.6→43.34 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3036819.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues THR 193 and GLU 201 are disordered in all chains.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.57 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→43.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.3 |