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- PDB-3cog: Crystal structure of human cystathionase (Cystathionine gamma lya... -

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Basic information

Entry
Database: PDB / ID: 3cog
TitleCrystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine
ComponentsCystathionine gamma-lyase
KeywordsLYASE / CTH / PLP / Propargylglycine / SGC / inhibitor / Structural Genomics / SGC Stockholm / Structural Genomics Consortium / Amino-acid biosynthesis / Cysteine biosynthesis / Disease mutation / Phosphoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase / homocysteine desulfhydrase activity / Cysteine formation from homocysteine / Degradation of cysteine and homocysteine / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) ...protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase / homocysteine desulfhydrase activity / Cysteine formation from homocysteine / Degradation of cysteine and homocysteine / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / hydrogen sulfide biosynthetic process / L-cysteine desulfhydrase activity / cysteine biosynthetic process / cysteine metabolic process / transsulfuration / negative regulation of apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to leukemia inhibitory factor / lipid metabolic process / pyridoxal phosphate binding / positive regulation of canonical NF-kappaB signal transduction / protein homotetramerization / calmodulin binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminopent-4-enoic acid / NITRATE ION / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCollins, R. / Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Collins, R. / Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Schuler, H. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Sagermark, J. / Busam, R.D. / Welin, M. / Weigelt, J. / Wikstrom, M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S.
Authors: Sun, Q. / Collins, R. / Huang, S. / Holmberg-Schiavone, L. / Anand, G.S. / Tan, C.H. / van-den-Berg, S. / Deng, L.W. / Moore, P.K. / Karlberg, T. / Sivaraman, J.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,18219
Polymers177,3434
Non-polymers1,83915
Water20,8971160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17860 Å2
ΔGint-120.1 kcal/mol
Surface area44930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.350, 107.220, 153.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cystathionine gamma-lyase / Gamma-cystathionase


Mass: 44335.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32929, cystathionine gamma-lyase

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Non-polymers , 6 types, 1175 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-2AG / (2S)-2-aminopent-4-enoic acid / L-allylglycine


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO2 / Comment: inhibitor*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAUTHORS STATE THAT THIS ENTRY IS A COMPLEX WITH DL-PROPARGYLGLYCINE. ACCORDING TO AUTHORS, THE ...AUTHORS STATE THAT THIS ENTRY IS A COMPLEX WITH DL-PROPARGYLGLYCINE. ACCORDING TO AUTHORS, THE LIGAND 2AG DOES NOT CONTAIN THE PROPARGYL GROUP BECAUSE THE CARBON AT THE PROXIMAL END OF THE TRIPLE BOND FORMS A BOND WITH THE ADJACENT TYROSINE, AND, THEREFORE, THE LIGAND INSTEAD CONTAINS A DOUBLE BOND BETWEEN THIS CARBON AND THE TERMINAL CARBON.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.2M Di-ammonium hydrogen citrate, 20% PEG 3350. Streak seeding used, apo crystal soaked with inhibitor, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Double mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 109200 / Num. obs: 109200 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 13.81
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.445 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NMP

2nmp


Resolution: 2→19.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.356 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20406 5460 5 %RANDOM
Rwork0.15831 ---
obs0.16061 103738 100 %-
all-103738 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.036 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11836 0 118 1160 13114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212263
X-RAY DIFFRACTIONr_bond_other_d0.0020.028164
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.96716629
X-RAY DIFFRACTIONr_angle_other_deg0.931320006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20151534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61824.397514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.029152046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561550
X-RAY DIFFRACTIONr_chiral_restr0.1190.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022362
X-RAY DIFFRACTIONr_nbd_refined0.2070.22698
X-RAY DIFFRACTIONr_nbd_other0.1960.28906
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25977
X-RAY DIFFRACTIONr_nbtor_other0.0890.26173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8081.58238
X-RAY DIFFRACTIONr_mcbond_other0.1771.53097
X-RAY DIFFRACTIONr_mcangle_it1.189212357
X-RAY DIFFRACTIONr_scbond_it1.99934976
X-RAY DIFFRACTIONr_scangle_it2.8964.54268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 417 -
Rwork0.185 7936 -
obs--100 %

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