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- PDB-6vju: Crystal Structure of Cystathionine beta synthase from Legionella ... -

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Basic information

Entry
Database: PDB / ID: 6vju
TitleCrystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Components(Cystathionine beta- ...) x 2
KeywordsLYASE / SSGCID / PLP / LLP / synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / : / lyase activity
Similarity search - Function
Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase / cysteine synthase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Authors: Bolejack, M.J. / Davies, D.R. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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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)72,50221
Polymers71,0852
Non-polymers1,41619
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-7 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.350, 91.790, 93.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 30 or resid 32...
21(chain B and (resid 9 through 30 or resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 30 or resid 32...A9 - 30
121(chain A and (resid 9 through 30 or resid 32...A32 - 50
131(chain A and (resid 9 through 30 or resid 32...A52 - 63
141(chain A and (resid 9 through 30 or resid 32...A8 - 324
151(chain A and (resid 9 through 30 or resid 32...A0
161(chain A and (resid 9 through 30 or resid 32...A0
171(chain A and (resid 9 through 30 or resid 32...A8 - 324
181(chain A and (resid 9 through 30 or resid 32...A134 - 136
191(chain A and (resid 9 through 30 or resid 32...A8 - 324
1101(chain A and (resid 9 through 30 or resid 32...A150 - 226
1111(chain A and (resid 9 through 30 or resid 32...A293 - 91
1121(chain A and (resid 9 through 30 or resid 32...A293
1131(chain A and (resid 9 through 30 or resid 32...A8 - 324
1141(chain A and (resid 9 through 30 or resid 32...A8 - 324
1151(chain A and (resid 9 through 30 or resid 32...A8 - 324
1161(chain A and (resid 9 through 30 or resid 32...A8 - 324
211(chain B and (resid 9 through 30 or resid 32...B9 - 30
221(chain B and (resid 9 through 30 or resid 32...B32 - 50
231(chain B and (resid 9 through 30 or resid 32...B52 - 63
241(chain B and (resid 9 through 30 or resid 32...B65 - 98
251(chain B and (resid 9 through 30 or resid 32...B100
261(chain B and (resid 9 through 30 or resid 32...B102 - 110
271(chain B and (resid 9 through 30 or resid 32...B112 - 125
281(chain B and (resid 9 through 30 or resid 32...B126 - 128
291(chain B and (resid 9 through 30 or resid 32...B8 - 324
2101(chain B and (resid 9 through 30 or resid 32...B8 - 324
2111(chain B and (resid 9 through 30 or resid 32...B8 - 324
2121(chain B and (resid 9 through 30 or resid 32...B8 - 324

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Components

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Cystathionine beta- ... , 2 types, 2 molecules AB

#1: Protein Cystathionine beta-lyase


Mass: 35656.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_14920, DI056_06925, DI105_06930 / Plasmid: LepnA.01147.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F0T8, UniProt: Q5ZRD1*PLUS
#2: Protein Cystathionine beta-lyase


Mass: 35428.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_14920, DI056_06925, DI105_06930 / Plasmid: LepnA.01147.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F0T8, UniProt: Q5ZRD1*PLUS

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Non-polymers , 5 types, 617 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: LepnA.01147.a.B1.PW38321 was crystallized at 19.49 mg/ml with 4 mM PLP, 4 mM serine, and 4 mM homocysteine and mixed 1:1 with 0.1 M ammonium acetate, 0.1 M Bis-Tris HCl pH 5.5, and 17% (w/v) ...Details: LepnA.01147.a.B1.PW38321 was crystallized at 19.49 mg/ml with 4 mM PLP, 4 mM serine, and 4 mM homocysteine and mixed 1:1 with 0.1 M ammonium acetate, 0.1 M Bis-Tris HCl pH 5.5, and 17% (w/v) PEG 10000. Cryo: 25% EG with 4 mM each ligand. Tray 3295506c1: puck mhb1-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→41.22 Å / Num. obs: 138423 / % possible obs: 99.7 % / Redundancy: 5.269 % / Biso Wilson estimate: 20.203 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 1.066 / Net I/σ(I): 15.68 / Num. measured all: 729374 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.334.9990.5352.565091910194101860.8930.59999.9
1.33-1.375.2670.4862.9952188991399090.8970.54100
1.37-1.415.2880.4053.5951058966196560.9240.4599.9
1.41-1.455.3040.324.5149490933493300.9520.355100
1.45-1.55.2970.2475.7848132908990860.9720.274100
1.5-1.555.3120.1997.2746687879587890.9780.22199.9
1.55-1.615.3130.168.9645244851885150.9860.177100
1.61-1.685.3230.12711.1643567819181840.9910.14199.9
1.68-1.755.3280.10413.5341710783578280.9930.11599.9
1.75-1.845.3230.08616.440242756675600.9950.09699.9
1.84-1.945.3230.06720.8437924713971250.9960.07499.8
1.94-2.065.2990.05824.5635859677867670.9970.06499.8
2.06-2.25.2670.0527.8433681640263950.9970.05699.9
2.2-2.375.2810.04530.7331465597459580.9980.0599.7
2.37-2.65.2750.04132.9728941550754860.9980.04599.6
2.6-2.915.2830.03835.2126197499849590.9980.04299.2
2.91-3.365.2570.03437.323178445144090.9990.03899.1
3.36-4.115.2470.03239.5119549378537260.9990.03598.4
4.11-5.815.2460.0340.1815219296929010.9990.03397.7
5.81-41.224.9120.02938.618124173616540.9980.03295.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4coo

4coo


Resolution: 1.3→41.22 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 1955 1.41 %
Rwork0.1484 136388 -
obs0.1489 138343 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 20.8074 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 1.3→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 111 598 5519
Biso mean--42.4 32.52 -
Num. residues----634
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2748X-RAY DIFFRACTION5.1TORSIONAL
12B2748X-RAY DIFFRACTION5.1TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.330.24711460.225496549800100
1.33-1.370.24761330.211996449777100
1.37-1.410.25721470.196296619808100
1.41-1.450.26451520.177796689820100
1.45-1.510.17191250.158996969821100
1.51-1.570.16231380.147596739811100
1.57-1.640.19741320.139697549886100
1.64-1.720.17971250.137397179842100
1.72-1.830.19571640.145797039867100
1.83-1.970.16851250.138797679892100
1.97-2.170.1991480.142697779925100
2.17-2.490.17141420.146598259967100
2.49-3.130.16951230.15189860998399
3.13-41.220.15981550.137699891014498

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