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- PDB-6y21: Crystal structure of delta466-491 cystathionine beta-synthase fro... -

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Basic information

Entry
Database: PDB / ID: 6y21
TitleCrystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with L-Cystathionine
ComponentsCystathionine beta-synthase
KeywordsCYTOSOLIC PROTEIN / Transulfuration / cystathionine / hydrogen sulfide / CBS / homocysteine / serine
Function / homology
Function and homology information


cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain ...Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Chem-P1T / Cystathionine beta-synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Quintana, I. / Martinez-Chantar, M. / Astegno, A. / Martinez-Cruz, L.A.
Funding support Spain, 4items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BFU2013-47531-R Spain
Ministry of Economy and Competitiveness (MINECO)BES-2014-068464 Spain
Ministry of Economy and Competitiveness (MINECO)BFU2016-77408-R Spain
Ministry of Economy and Competitiveness (MINECO)BES-2017-080435 Spain
CitationJournal: To Be Published
Title: Cystathionine Beta-synthase from Toxoplasma gondii with PLP-Cystathionine
Authors: Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Quintana, I. / Martinez-Chantar, M. / Astegno, A. / Martinez-Cruz, L.A.
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cystathionine beta-synthase
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8296
Polymers167,8753
Non-polymers9553
Water00
1
D: Cystathionine beta-synthase
hetero molecules

D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5534
Polymers111,9172
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8750 Å2
ΔGint-46 kcal/mol
Surface area36830 Å2
MethodPISA
2
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5534
Polymers111,9172
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-46 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.006, 83.006, 421.373
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 158 or (resid 159...
21(chain B and (resid 6 through 193 or (resid 194...
31(chain D and (resid 6 through 158 or (resid 159...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain A and (resid 6 through 158 or (resid 159...AB6 - 1586 - 158
12GLNGLNGLNGLN(chain A and (resid 6 through 158 or (resid 159...AB159159
13ALAALAP1TP1T(chain A and (resid 6 through 158 or (resid 159...AB - E6 - 6016
14ALAALAP1TP1T(chain A and (resid 6 through 158 or (resid 159...AB - E6 - 6016
15ALAALAP1TP1T(chain A and (resid 6 through 158 or (resid 159...AB - E6 - 6016
16ALAALAP1TP1T(chain A and (resid 6 through 158 or (resid 159...AB - E6 - 6016
21ALAALAGLYGLY(chain B and (resid 6 through 193 or (resid 194...BC6 - 1936 - 193
22THRTHRTHRTHR(chain B and (resid 6 through 193 or (resid 194...BC194194
23ALAALAP1TP1T(chain B and (resid 6 through 193 or (resid 194...BC - F6 - 6016
24ALAALAP1TP1T(chain B and (resid 6 through 193 or (resid 194...BC - F6 - 6016
25ALAALAP1TP1T(chain B and (resid 6 through 193 or (resid 194...BC - F6 - 6016
26ALAALAP1TP1T(chain B and (resid 6 through 193 or (resid 194...BC - F6 - 6016
31ALAALAASPASP(chain D and (resid 6 through 158 or (resid 159...DA6 - 1586 - 158
32GLNGLNGLNGLN(chain D and (resid 6 through 158 or (resid 159...DA159159
33ALAALAP1TP1T(chain D and (resid 6 through 158 or (resid 159...DA - D6 - 6016
34ALAALAP1TP1T(chain D and (resid 6 through 158 or (resid 159...DA - D6 - 6016
35ALAALAP1TP1T(chain D and (resid 6 through 158 or (resid 159...DA - D6 - 6016
36ALAALAP1TP1T(chain D and (resid 6 through 158 or (resid 159...DA - D6 - 6016

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Components

#1: Protein Cystathionine beta-synthase


Mass: 55958.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Gene: TGME49_259180 / Production host: Toxoplasma gondii ME49 (eukaryote)
References: UniProt: A0A125YSJ9, cystathionine beta-synthase
#2: Chemical ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: 9% PEG 3350, 0.1M MES pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.547→210.687 Å / Num. obs: 17599 / % possible obs: 90.8 % / Redundancy: 18.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.055 / Rrim(I) all: 0.235 / Net I/σ(I): 11.4 / Num. measured all: 327391
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.547-3.80119.12.695168088820.490.632.7691.451.1
10.959-210.68614.20.064124398780.990.0170.06732.799.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBQ

1jbq


Resolution: 3.6→68.034 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.72
RfactorNum. reflection% reflection
Rfree0.2905 836 4.79 %
Rwork0.2626 --
obs0.2639 17444 84.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.85 Å2 / Biso mean: 107.1945 Å2 / Biso min: 68.52 Å2
Refinement stepCycle: final / Resolution: 3.6→68.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 63 0 10787
Biso mean--86.59 --
Num. residues----1425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6836X-RAY DIFFRACTION4.58TORSIONAL
12B6836X-RAY DIFFRACTION4.58TORSIONAL
13D6836X-RAY DIFFRACTION4.58TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6005-3.8260.3784440.341790429
3.826-4.12140.29851460.3219246677
4.1214-4.53610.30151620.28593204100
4.5361-5.19230.28561420.26653275100
5.1923-6.54090.33481710.28683284100
6.5409-67.980.2571710.22153475100
Refinement TLS params.Method: refined / Origin x: 18.9562 Å / Origin y: 5.6448 Å / Origin z: 36.8919 Å
111213212223313233
T0.8103 Å2-0.1424 Å2-0.0466 Å2-0.6666 Å2-0.0658 Å2--0.9597 Å2
L0.5438 °2-0.4071 °2-0.285 °2-0.0036 °20.0098 °2--0.6362 °2
S0.067 Å °0.0053 Å °-0.0181 Å °0.016 Å °-0.1207 Å °-0.0237 Å °0.1483 Å °0.02 Å °0.047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD6 - 601
2X-RAY DIFFRACTION1allA6 - 601
3X-RAY DIFFRACTION1allB6 - 601

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