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- PDB-8sa9: Crystal Structure of Cystathionine beta lyase from Klebsiella aer... -

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Basic information

Entry
Database: PDB / ID: 8sa9
TitleCrystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP-Oxamate Adduct (C2 form)
ComponentsCystathionine beta-lyase
KeywordsLYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
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
CITRATE ANION / PYRIDOXAL-5'-PHOSPHATE / Chem-ZTS / Cystathionine beta-lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP-Oxamate Adduct (C2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,5287
Polymers88,2042
Non-polymers1,3245
Water17,799988
1
A: Cystathionine beta-lyase
B: Cystathionine beta-lyase
hetero molecules

A: Cystathionine beta-lyase
B: Cystathionine beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,05714
Polymers176,4094
Non-polymers2,64810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area21040 Å2
ΔGint-110 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.313, 131.511, 82.585
Angle α, β, γ (deg.)90.00, 103.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-917-

HOH

31B-670-

HOH

41B-961-

HOH

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Components

#1: Protein Cystathionine beta-lyase


Mass: 44102.242 Da / Num. of mol.: 2 / Mutation: V244I, L360P
Source method: isolated from a genetically manipulated source
Details: Covalent linkage between LYS 210 NZ atom and PLP C4A and PLP adduct formed with oxamate. Present in a 10/90 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
#2: Chemical ChemComp-ZTS / [({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino](oxo)acetic acid


Mass: 320.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpueus G9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium ...Details: Morpueus G9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Tris/BICINE, pH 8.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate, 2mM PLP added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13220, well G9 drop 3, Puck: PSL-0416, 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: 1.1→80.2 Å / Num. obs: 345136 / % possible obs: 94.7 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 1.02 / Net I/σ(I): 12.4 / Num. measured all: 2207969
Reflection shellResolution: 1.1→1.13 Å / % possible obs: 58.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 1.056 / Num. measured all: 59166 / Num. unique obs: 15798 / CC1/2: 0.574 / Rpim(I) all: 0.617 / Rrim(I) all: 1.229 / Χ2: 1.03 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4906: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→26.86 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.137 17102 4.96 %
Rwork0.1246 --
obs0.1252 345024 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 85 988 7088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086550
X-RAY DIFFRACTIONf_angle_d1.0238942
X-RAY DIFFRACTIONf_dihedral_angle_d12.8232388
X-RAY DIFFRACTIONf_chiral_restr0.082989
X-RAY DIFFRACTIONf_plane_restr0.0121180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.29923110.27286225X-RAY DIFFRACTION54
1.11-1.130.26273410.25847131X-RAY DIFFRACTION61
1.13-1.140.26014120.24117972X-RAY DIFFRACTION69
1.14-1.150.23815000.23378845X-RAY DIFFRACTION77
1.15-1.170.2335600.21639833X-RAY DIFFRACTION85
1.17-1.180.2315240.209510820X-RAY DIFFRACTION94
1.18-1.20.20996170.193611412X-RAY DIFFRACTION99
1.2-1.220.19786210.176211525X-RAY DIFFRACTION100
1.22-1.240.1846130.165811521X-RAY DIFFRACTION100
1.24-1.260.17845470.161111530X-RAY DIFFRACTION100
1.26-1.280.1775330.152911628X-RAY DIFFRACTION100
1.28-1.30.1655440.14911600X-RAY DIFFRACTION100
1.3-1.330.1666070.142211510X-RAY DIFFRACTION100
1.33-1.360.15726010.133711545X-RAY DIFFRACTION100
1.36-1.390.15626030.132211555X-RAY DIFFRACTION100
1.39-1.420.16185970.123111514X-RAY DIFFRACTION100
1.42-1.450.13186200.117711519X-RAY DIFFRACTION100
1.45-1.490.13016210.113711517X-RAY DIFFRACTION100
1.49-1.540.12956340.107411511X-RAY DIFFRACTION100
1.54-1.590.12736530.102411516X-RAY DIFFRACTION100
1.59-1.640.12616070.098711548X-RAY DIFFRACTION100
1.64-1.710.1136000.100511546X-RAY DIFFRACTION100
1.71-1.790.12275880.108211560X-RAY DIFFRACTION100
1.79-1.880.136210.111211519X-RAY DIFFRACTION100
1.88-20.12566190.111511542X-RAY DIFFRACTION100
2-2.150.11756320.107111521X-RAY DIFFRACTION100
2.15-2.370.11886250.105411543X-RAY DIFFRACTION100
2.37-2.710.12775620.109911629X-RAY DIFFRACTION100
2.71-3.420.13976100.124211598X-RAY DIFFRACTION100
3.42-26.860.11885790.127211687X-RAY DIFFRACTION100

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