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- PDB-8u98: Crystal Structure of Cystathionine beta lyase from Klebsiella aer... -

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Basic information

Entry
Database: PDB / ID: 8u98
TitleCrystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Glycine adduct)
ComponentsCystathionine beta-lyase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / transsulfuration / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
Cystathionine beta-lyase, bacterial / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
GLYCINE / PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Glycine adduct)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)178,81530
Polymers176,4094
Non-polymers2,40626
Water27,1671508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24110 Å2
ΔGint-53 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.924, 133.051, 87.494
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cystathionine beta-lyase


Mass: 44102.242 Da / Num. of mol.: 4 / Mutation: V244I, L360P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_03480 / Plasmid: KlaeA.00906.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FMF8, cystathionine beta-lyase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1508 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus E6: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM HEPES/MOPS, pH 7.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene ...Details: Morpheus E6: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM HEPES/MOPS, pH 7.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol, 2mM PLP and glycine added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13534 well E6 drop 2, Puck: PSL-0903, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→102.43 Å / Num. obs: 359218 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 15.4 / Num. measured all: 2484245
Reflection shellResolution: 1.4→1.44 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.018 / Num. measured all: 185109 / Num. unique obs: 26567 / CC1/2: 0.809 / Rpim(I) all: 0.414 / Rrim(I) all: 1.1 / Χ2: 1.04 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→24.82 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1615 17924 4.99 %
Rwork0.135 --
obs0.1363 358875 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11982 0 152 1508 13642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713097
X-RAY DIFFRACTIONf_angle_d0.91717837
X-RAY DIFFRACTIONf_dihedral_angle_d13.3024735
X-RAY DIFFRACTIONf_chiral_restr0.0721969
X-RAY DIFFRACTIONf_plane_restr0.012340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.27445570.257311410X-RAY DIFFRACTION100
1.42-1.430.25616210.226511311X-RAY DIFFRACTION100
1.43-1.450.25836200.21711279X-RAY DIFFRACTION100
1.45-1.470.2456010.211111314X-RAY DIFFRACTION100
1.47-1.490.22636040.195411388X-RAY DIFFRACTION100
1.49-1.510.23156450.192411300X-RAY DIFFRACTION100
1.51-1.530.2185930.174311330X-RAY DIFFRACTION100
1.53-1.550.19615820.166711344X-RAY DIFFRACTION100
1.55-1.580.1985810.1611369X-RAY DIFFRACTION100
1.58-1.60.20056010.155211334X-RAY DIFFRACTION100
1.6-1.630.18885860.146911320X-RAY DIFFRACTION100
1.63-1.660.16776010.132911374X-RAY DIFFRACTION100
1.66-1.690.15185860.125811370X-RAY DIFFRACTION100
1.69-1.730.17475980.126211382X-RAY DIFFRACTION100
1.73-1.760.16016490.123311242X-RAY DIFFRACTION100
1.76-1.80.15675810.121511419X-RAY DIFFRACTION100
1.8-1.850.17155780.126411352X-RAY DIFFRACTION100
1.85-1.90.16625630.125811462X-RAY DIFFRACTION100
1.9-1.960.15775640.122611305X-RAY DIFFRACTION100
1.96-2.020.16325620.127311428X-RAY DIFFRACTION100
2.02-2.090.16616280.128811393X-RAY DIFFRACTION100
2.09-2.170.15276630.122811294X-RAY DIFFRACTION100
2.17-2.270.13796080.118611363X-RAY DIFFRACTION100
2.27-2.390.13785920.116611369X-RAY DIFFRACTION100
2.39-2.540.14055800.118611427X-RAY DIFFRACTION100
2.54-2.740.14435890.121911398X-RAY DIFFRACTION100
2.74-3.010.1456200.127211351X-RAY DIFFRACTION100
3.01-3.450.15715610.134711442X-RAY DIFFRACTION100
3.45-4.340.15496310.129811428X-RAY DIFFRACTION100
4.34-24.820.15775790.144711453X-RAY DIFFRACTION99

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