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- PDB-21kb: Cystathionine beta-lyase from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 21kb
TitleCystathionine beta-lyase from Klebsiella pneumoniae
Componentscysteine-S-conjugate beta-lyase
KeywordsLYASE / Bacterial cystathionine beta-lyase / kCBL / holoenzyme / PLP-bounded form / Klebsiella pneumoniae
Function / homology
Function and homology information


: / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / transsulfuration / : / pyridoxal phosphate binding / cytoplasm
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
DI(HYDROXYETHYL)ETHER / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVarfolomeeva, L.A. / Anufrieva, N.V. / Morozova, E.A. / Puchkov, V.M. / Kulikova, V.V. / Revtovich, S.V. / Minyaev, M.E. / Popov, V.O. / Solyev, P.N. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2025-454 Russian Federation
CitationJournal: Mol Catal / Year: 2026
Title: Klebsiella pneumoniae cystathionine beta-lyase-structure-functional analysis of a promising component of the enzyme-prodrug binary system
Authors: Anufrieva, N.V. / Morozova, E.A. / Puchkov, V.M. / Tkachev, Y.V. / Kulikova, V.V. / Revtovich, S.V. / Mitkevich, V.A. / Makarov, A.A. / Minyaev, M.E. / Varfolomeeva, L.A. / Popov, V.O. / ...Authors: Anufrieva, N.V. / Morozova, E.A. / Puchkov, V.M. / Tkachev, Y.V. / Kulikova, V.V. / Revtovich, S.V. / Mitkevich, V.A. / Makarov, A.A. / Minyaev, M.E. / Varfolomeeva, L.A. / Popov, V.O. / Boyko, K.M. / Solyev, P.N.
History
DepositionDec 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cysteine-S-conjugate beta-lyase
B: cysteine-S-conjugate beta-lyase
C: cysteine-S-conjugate beta-lyase
D: cysteine-S-conjugate beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4209
Polymers173,8734
Non-polymers5475
Water27,6171533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-84 kcal/mol
Surface area45950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.418, 131.209, 84.574
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
cysteine-S-conjugate beta-lyase


Mass: 43468.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: metC, metC_1, metC_2, metC_4, B5L96_16180, B6I68_11540, BANRA_02509, BL124_00018915, CP554_04135, DM078_01535, DW286_17480, E1814_21630, EAO17_10070, FXN67_07235, G4V31_19190, GJJ01_08005, ...Gene: metC, metC_1, metC_2, metC_4, B5L96_16180, B6I68_11540, BANRA_02509, BL124_00018915, CP554_04135, DM078_01535, DW286_17480, E1814_21630, EAO17_10070, FXN67_07235, G4V31_19190, GJJ01_08005, GJJ08_003585, GNF00_15520, H3G96_024120, JMZ77_03585, LS45_25460, NCTC11679_00773, NCTC13443_06402, NCTC204_02949, NCTC5051_04552, NCTC5052_04013, NCTC5053_05113, NCTC8849_05374, NCTC9601_00031, NCTC9637_01279, Q6294_05520, SAMEA104567804_01826, SAMEA3499874_00682, SAMEA3499901_04217, SAMEA3515122_03450, SAMEA3538828_04005, SAMEA3649591_00131, SAMEA3649733_03630, SAMEA3720909_03545, SAMEA3729652_02328, SAMEA4873632_04081
Production host: Escherichia coli (E. coli)
References: UniProt: Q0ZBA0, cysteine-S-conjugate beta-lyase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop
Details: 50 mM TRIS-HCl, pH 8.5, 55% PEG MME 2000, 0.2 mM PLP, 25 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22.89 Å / Num. obs: 136224 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Χ2: 1.07 / Net I/σ(I): 17.2 / Num. measured all: 919184
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 96.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.373 / Num. measured all: 43236 / Num. unique obs: 6625 / CC1/2: 0.941 / Rpim(I) all: 0.155 / Rrim(I) all: 0.405 / Χ2: 0.9 / Net I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.934 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20458 6902 5.1 %RANDOM
Rwork0.16629 ---
obs0.16822 129090 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.061 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å20.69 Å2
2---0.57 Å20 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.9→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12037 0 88 1533 13658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01212444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.816885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67751561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.751594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.716102011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.21897
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4621.2876257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9882.3057813
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6321.4976187
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.95915.820720
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 507 -
Rwork0.215 9313 -
obs--96.37 %

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