+Open data
-Basic information
Entry | Database: PDB / ID: 1m54 | ||||||
---|---|---|---|---|---|---|---|
Title | CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS | ||||||
Components | CYSTATHIONINE BETA-SYNTHASE | ||||||
Keywords | LYASE / PLP PROTEIN FOLD TYPE II (TRYPTOPHAN SYNTHASE) / PLP AND HEME BOUND TO PROTEIN / REDUCED VICINAL CYSTEINES | ||||||
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: 2.9 Å | ||||||
Authors | Taoka, S. / Lepore, B.W. / Kabil, O. / Ojha, S. / Ringe, D. / Banerjee, R. | ||||||
Citation | Journal: BIOCHEMISTRY / Year: 2002 Title: HUMAN CYSTATHIONINE BETA-SYNTHASE IS A HEME SENSOR PROTEIN. EVIDENCE THAT THE REDOX SENSOR IS HEME AND NOT THE VICINAL CYSTEINES IN THE CXXC MOTIF SEEN IN THE CRYSTAL STRUCTURE OF THE TRUNCATED ENZYME Authors: Taoka, S. / Lepore, B.W. / Kabil, O. / Ojha, S. / Ringe, D. / Banerjee, R. #1: Journal: Embo J. / Year: 2001 Title: STRUCTURE OF HUMAN CYSTATHIONINE-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE-DEPENDENT HEME PROTEIN Authors: Meier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m54.cif.gz | 402.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m54.ent.gz | 339.2 KB | Display | PDB format |
PDBx/mmJSON format | 1m54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m54_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1m54_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1m54_validation.xml.gz | 109.4 KB | Display | |
Data in CIF | 1m54_validation.cif.gz | 140.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m54 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m54 | HTTPS FTP |
-Related structure data
Related structure data | 1jbqS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | the biologically relevant entity is a dimer. three dimers occupy the assymetric unit. chain A is related to chain B by the followin 3x3 matrix: ( 0.78094 -0.51950 -0.34677 ) ( -0.51627 -0.84936 0.10976 ) ( -0.35155 0.09331 -0.93151 ) translation: (-0.12746 -0.20056 -0.68113) |
-Components
#1: Protein | Mass: 39922.727 Da / Num. of mol.: 6 / Fragment: RESIDUES 44-406 / Mutation: I44M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Organ: blood / Plasmid: pCBS-deltaN43/deltaC143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35520, cystathionine beta-synthase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.83 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 10K, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.7401, 1.7372 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2001 / Details: Bent cylindrical Si-mirror (Rh coating) | |||||||||
Radiation | Monochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.9→50 Å / Num. all: 87507 / Num. obs: 87507 / % possible obs: 83.2 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 58.127 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 9.2 | |||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3 / Num. unique all: 53028 / Rsym value: 0.459 / % possible all: 10 | |||||||||
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 53028 / % possible obs: 93.8 % / Num. measured all: 628994 / Rmerge(I) obs: 0.14 | |||||||||
Reflection shell | *PLUS Highest resolution: 2.9 Å / % possible obs: 93.2 % / Rmerge(I) obs: 0.459 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JBQ Resolution: 2.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. reflection all: 628994 / Num. reflection obs: 53028 / Num. reflection Rfree: 8143 / % reflection Rfree: 7.7 % / Rfactor Rfree: 0.348 / Rfactor Rwork: 0.259 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.405 / Rfactor Rwork: 0.336 |