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

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Basic information

Entry
Database: PDB / ID: 8sab
TitleCrystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP adduct with Alanine (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 / 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
LYSINE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / ALANYL-PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 adduct with Alanine (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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,65217
Polymers88,2042
Non-polymers2,44715
Water11,025612
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)181,30434
Polymers176,4094
Non-polymers4,89530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area26900 Å2
ΔGint-251 kcal/mol
Surface area43650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.325, 130.522, 82.366
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

21A-759-

HOH

31B-583-

HOH

41B-690-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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 Alanine. 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

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Non-polymers , 8 types, 627 molecules

#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpueus H12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride ...Details: Morpueus H12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. 2mM PLP and 2mM Arginine added to protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13220 well H12 drop 3, Puck: PSL-0506, 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: 1.6→79.93 Å / Num. obs: 116919 / % possible obs: 99.5 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.041 / Rrim(I) all: 0.1 / Χ2: 0.99 / Net I/σ(I): 11.7 / Num. measured all: 667211
Reflection shellResolution: 1.6→1.64 Å / % possible obs: 98.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.036 / Num. measured all: 50244 / Num. unique obs: 8555 / CC1/2: 0.659 / Rpim(I) all: 0.462 / Rrim(I) all: 1.136 / Χ2: 1.01 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.18 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1817 5773 4.94 %
Rwork0.159 --
obs0.1602 116867 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 159 612 6782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046544
X-RAY DIFFRACTIONf_angle_d0.7728923
X-RAY DIFFRACTIONf_dihedral_angle_d12.8532360
X-RAY DIFFRACTIONf_chiral_restr0.045992
X-RAY DIFFRACTIONf_plane_restr0.0081156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28631820.25863643X-RAY DIFFRACTION99
1.62-1.640.22981810.26123713X-RAY DIFFRACTION99
1.64-1.660.27421820.25133659X-RAY DIFFRACTION99
1.66-1.680.27672270.23353626X-RAY DIFFRACTION99
1.68-1.70.25481850.23463672X-RAY DIFFRACTION99
1.7-1.720.26871710.2283690X-RAY DIFFRACTION99
1.72-1.750.22921950.22513698X-RAY DIFFRACTION99
1.75-1.770.2631790.22383678X-RAY DIFFRACTION99
1.77-1.80.22591970.213681X-RAY DIFFRACTION99
1.8-1.830.24711850.21053739X-RAY DIFFRACTION99
1.83-1.860.24351890.21113685X-RAY DIFFRACTION99
1.86-1.90.24181710.19743709X-RAY DIFFRACTION99
1.9-1.930.22831800.19093671X-RAY DIFFRACTION99
1.93-1.970.22382080.19133712X-RAY DIFFRACTION100
1.97-2.020.19732160.18273690X-RAY DIFFRACTION100
2.02-2.060.21031930.18033704X-RAY DIFFRACTION100
2.06-2.110.20212030.17643693X-RAY DIFFRACTION100
2.11-2.170.21481940.17933721X-RAY DIFFRACTION100
2.17-2.240.22551750.17283723X-RAY DIFFRACTION100
2.24-2.310.19622090.16783705X-RAY DIFFRACTION100
2.31-2.390.18612190.15763679X-RAY DIFFRACTION100
2.39-2.490.19151730.14843733X-RAY DIFFRACTION100
2.49-2.60.17161940.14433711X-RAY DIFFRACTION100
2.6-2.740.14041760.14283747X-RAY DIFFRACTION100
2.74-2.910.17131920.1463742X-RAY DIFFRACTION100
2.91-3.130.15552190.14423687X-RAY DIFFRACTION100
3.13-3.450.14361910.13193740X-RAY DIFFRACTION100
3.45-3.940.14111970.12013741X-RAY DIFFRACTION100
3.94-4.970.11881880.10793747X-RAY DIFFRACTION100
4.97-34.180.17442020.14933755X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.644-0.0657-0.57911.634-0.25323.05630.0755-0.0627-0.01550.01040.0380.14840.0639-0.3462-0.1230.082-0.02180.01680.17660.01010.144627.658-9.674-4.215
20.7976-0.1745-0.25430.6880.03960.9506-0.0564-0.17240.1460.07320.01020.0267-0.1085-0.13010.03240.12020.02420.020.1734-0.03960.143134.7398.33112.023
30.7215-0.0716-0.20070.19960.09470.5897-0.0123-0.36880.02320.0750.0103-0.0157-0.0052-0.12420.0070.1638-0.01240.02940.2966-0.00430.127243.489-5.12828.593
43.3287-0.4229-1.83.1664-0.44347.28550.06-0.3761-0.24060.2534-0.1054-0.05320.12780.15510.07030.139-0.0242-0.01910.1160.03140.159850.615-22.0716.977
50.09030.2944-0.10091.29280.19750.95910.1943-0.0458-0.2532-0.03490.0439-0.01030.30160.0825-0.1550.26310.0343-0.12530.14490.00340.289155.385-35.268.027
60.0055-0.01080.00290.07340.01480.00970.0876-0.0963-0.14840.0446-0.0182-0.06560.1101-0.01220.03480.5543-0.1936-0.28740.3290.1980.563134.242-53.31214.801
70.43280.5521-0.51312.3034-1.24972.17430.0684-0.0938-0.12360.0823-0.0835-0.27120.18630.07620.08550.3747-0.1456-0.19690.2710.16130.397740.113-43.09520.43
80.3468-0.4125-0.09721.4056-0.77410.89360.1601-0.0998-0.2770.17340.0263-0.12560.24790.025-0.13090.3072-0.0498-0.16270.15760.0330.339844.504-37.3489.095
90.25320.1788-0.16230.1256-0.11410.10230.1336-0.1765-0.1025-0.00510.0350.14280.1411-0.26830.06180.3036-0.1854-0.07170.4230.17950.297722.658-32.43119.101
100.9180.36720.02350.16950.09850.43750.1249-0.1022-0.14560.04720.00920.11990.1597-0.14810.05380.3148-0.1973-0.07370.3870.15020.304917.133-33.73312.233
115.93780.92251.20861.90390.6834.0072-0.09830.72130.0168-0.03990.0835-0.0087-0.05940.38640.01880.2849-0.03610.1060.07910.04580.119837.31-19.05612.132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:75 )A4 - 75
2X-RAY DIFFRACTION2( CHAIN A AND RESID 76:245 )A76 - 245
3X-RAY DIFFRACTION3( CHAIN A AND RESID 246:395 )A246 - 395
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:30 )B3 - 30
5X-RAY DIFFRACTION5( CHAIN B AND RESID 31:97 )B31 - 97
6X-RAY DIFFRACTION6( CHAIN B AND RESID 98:176 )B98 - 176
7X-RAY DIFFRACTION7( CHAIN B AND RESID 177:207 )B177 - 207
8X-RAY DIFFRACTION8( CHAIN B AND RESID 208:245 )B208 - 245
9X-RAY DIFFRACTION9( CHAIN B AND RESID 246:330 )B246 - 330
10X-RAY DIFFRACTION10( CHAIN B AND RESID 331:395 )B331 - 395
11X-RAY DIFFRACTION11( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )A401
12X-RAY DIFFRACTION11( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )B401

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