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- PDB-8sa8: Crystal Structure of Cystathionine beta lyase from Klebsiella aer... -

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Basic information

Entry
Database: PDB / ID: 8sa8
TitleCrystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, Covalently bound and free PLP (I2 form)
ComponentsCystathionine beta-lyase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / LYASE
Function / homology
Function and homology information


L-cysteine catabolic process to pyruvate / cystathionine 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
PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSeattle 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)HHSN272201700059C 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 (I2 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.
History
DepositionMar 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 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)179,91153
Polymers176,4094
Non-polymers3,50249
Water30,7881709
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.887, 131.544, 165.363
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cystathionine beta-lyase


Mass: 44102.242 Da / Num. of mol.: 4 / Mutation: V244I, L360P
Source method: isolated from a genetically manipulated source
Details: Covalent linkage between LYS 210 NZ atom and PLP C4A. Active site contains the covalent attached PLP and free PLP in a 50/50 ratio
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_03480 / Plasmid: KlaeA.00906.a.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FMF8, cystathionine beta-lyase

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Non-polymers , 5 types, 1758 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1709 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpueus A10: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2, 2mM PLP added to the protein prior to crystallization, KlaeA.00906.a.B1. ...Details: Morpueus A10: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Tris/BICINE, pH 8.5, 30 mM MgCl2 and 30 mM CaCl2, 2mM PLP added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13219, well A10 drop 2, Puck: PSL-0412, 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: Feb 14, 2022
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: 1.3→101.64 Å / Num. obs: 425218 / % possible obs: 95.8 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 3067480
Reflection shellResolution: 1.3→1.33 Å / % possible obs: 93 % / Redundancy: 7.5 % / Rmerge(I) obs: 1.668 / Num. measured all: 227574 / Num. unique obs: 30496 / CC1/2: 0.607 / Rpim(I) all: 0.653 / Rrim(I) all: 1.792 / Χ2: 1.03 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4906: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→21.22 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1525 21113 4.97 %
Rwork0.131 --
obs0.1321 424951 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11984 0 220 1709 13913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713169
X-RAY DIFFRACTIONf_angle_d1.0417913
X-RAY DIFFRACTIONf_dihedral_angle_d14.3394764
X-RAY DIFFRACTIONf_chiral_restr0.0751976
X-RAY DIFFRACTIONf_plane_restr0.0122346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.29156910.268713048X-RAY DIFFRACTION93
1.31-1.330.2766660.256613086X-RAY DIFFRACTION93
1.33-1.350.27436870.245913060X-RAY DIFFRACTION93
1.35-1.360.2637080.24413090X-RAY DIFFRACTION93
1.36-1.380.27537040.231313089X-RAY DIFFRACTION93
1.38-1.40.26026860.218113220X-RAY DIFFRACTION94
1.4-1.420.22056770.204113181X-RAY DIFFRACTION94
1.42-1.440.23666420.192613220X-RAY DIFFRACTION94
1.44-1.460.21686880.183213272X-RAY DIFFRACTION94
1.46-1.490.22036900.17313299X-RAY DIFFRACTION94
1.49-1.510.1946850.160213300X-RAY DIFFRACTION95
1.51-1.540.17067330.145813276X-RAY DIFFRACTION95
1.54-1.570.17576730.137213309X-RAY DIFFRACTION95
1.57-1.60.16746520.13113456X-RAY DIFFRACTION95
1.6-1.640.16387200.120213389X-RAY DIFFRACTION95
1.64-1.680.15097240.115713390X-RAY DIFFRACTION96
1.68-1.720.13697060.111713456X-RAY DIFFRACTION96
1.72-1.760.14317160.111513491X-RAY DIFFRACTION96
1.76-1.820.13787390.111813492X-RAY DIFFRACTION96
1.82-1.870.13966690.111613644X-RAY DIFFRACTION96
1.87-1.940.13846980.113613610X-RAY DIFFRACTION97
1.94-2.020.13747190.110913610X-RAY DIFFRACTION97
2.02-2.110.14117630.116413666X-RAY DIFFRACTION97
2.11-2.220.1437300.110713715X-RAY DIFFRACTION97
2.22-2.360.12616990.107413800X-RAY DIFFRACTION98
2.36-2.540.12557010.109613826X-RAY DIFFRACTION98
2.54-2.80.13477220.112813847X-RAY DIFFRACTION98
2.8-3.20.13477360.12213914X-RAY DIFFRACTION98
3.2-4.030.13857460.125313981X-RAY DIFFRACTION99
4.03-21.220.13897430.132914101X-RAY DIFFRACTION99

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