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- PDB-3elp: Structure of cystationine gamma lyase -

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Basic information

Entry
Database: PDB / ID: 3elp
TitleStructure of cystationine gamma lyase
ComponentsCystathionine gamma-lyase
KeywordsLYASE / alpha beta protein / Alternative splicing / Amino-acid biosynthesis / Cysteine biosynthesis / Cytoplasm / Disease mutation / Phosphoprotein / Polymorphism / 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 / protein homotetramerization / positive regulation of canonical NF-kappaB signal transduction / 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
Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSun, Q. / Sivaraman, J.
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
DepositionSep 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)180,0134
Polymers180,0134
Non-polymers00
Water8,413467
1
B: Cystathionine gamma-lyase
A: Cystathionine gamma-lyase

B: Cystathionine gamma-lyase
A: Cystathionine gamma-lyase


Theoretical massNumber of molelcules
Total (without water)180,0134
Polymers180,0134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area8500 Å2
ΔGint-46 kcal/mol
Surface area50660 Å2
MethodPISA
2
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase

C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase


Theoretical massNumber of molelcules
Total (without water)180,0134
Polymers180,0134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8490 Å2
ΔGint-46 kcal/mol
Surface area50710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.304, 121.304, 125.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 45003.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 / References: UniProt: P32929, cystathionine gamma-lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.08 % / Mosaicity: 0.564 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% (v/v) PEG 1000, 0.2M lithium sulfate, 0.1M phosphate-citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 71004 / % possible obs: 99.8 % / Observed criterion σ(I): -0.5 / Redundancy: 10.2 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.127 / Χ2: 1.036 / Net I/σ(I): 14.182
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.4-2.494.70.6762.170031.03998.8
2.49-2.596.50.65570441.03499.8
2.59-2.780.61770791.032100
2.7-2.859.10.53771001.012100
2.85-3.029.70.45170821.005100
3.02-3.2610.80.32770931.035100
3.26-3.5812.30.19671281.018100
3.58-4.113.20.11771131.02100
4.1-5.1713.70.0871421.056100
5.17-5013.90.04472201.08799.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å43.62 Å
Translation4 Å43.62 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NMP

2nmp


Resolution: 2.4→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.754 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3582 5.1 %RANDOM
Rwork0.222 66936 --
obs-70518 99.4 %-
Solvent computationBsol: 37.54 Å2
Displacement parametersBiso max: 119.4 Å2 / Biso mean: 49.79 Å2 / Biso min: 16.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.108 Å20 Å20 Å2
2---1.108 Å20 Å2
3---2.217 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10616 0 0 467 11083
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.383
X-RAY DIFFRACTIONc_mcbond_it1.9381.5
X-RAY DIFFRACTIONc_scbond_it3.032
X-RAY DIFFRACTIONc_mcangle_it3.3562
X-RAY DIFFRACTIONc_scangle_it5.1052.5
LS refinement shellResolution: 2.4→2.42 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.422 62 -
Rwork0.41 1404 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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