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

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Basic information

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


cystathionine beta-synthase / cystathionine beta-synthase activity / L-cysteine biosynthetic process via L-cystathionine / L-cysteine biosynthetic process from L-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 ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.151 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: Comput Struct Biotechnol J / Year: 2021
Title: Structural insight into the unique conformation of cystathionine beta-synthase from Toxoplasma gondii .
Authors: Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Nunez-Franco, R. / Gil-Pitarch, C. / Quintana, I. / Jimenez-Oses, G. / Dominici, P. / Martinez-Chantar, M.L. / ...Authors: Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Nunez-Franco, R. / Gil-Pitarch, C. / Quintana, I. / Jimenez-Oses, G. / Dominici, P. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A.
History
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _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
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
E: Cystathionine beta-synthase
F: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,65912
Polymers335,7506
Non-polymers1,9096
Water00
1
A: Cystathionine beta-synthase
F: 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 area8630 Å2
ΔGint-49 kcal/mol
Surface area36550 Å2
MethodPISA
2
B: Cystathionine beta-synthase
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
Buried area8680 Å2
ΔGint-46 kcal/mol
Surface area36740 Å2
MethodPISA
3
C: Cystathionine beta-synthase
E: 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 area8780 Å2
ΔGint-46 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.441, 82.441, 421.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 255 or (resid 256...
21(chain B and (resid 6 through 255 or (resid 256...
31(chain C and (resid 6 through 255 or (resid 256...
41(chain D and (resid 6 through 255 or (resid 256...
51(chain E and (resid 6 through 362 or resid 369...
61(chain F and (resid 6 through 255 or (resid 256...

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
11ALAALAARGARG(chain A and (resid 6 through 255 or (resid 256...AA6 - 2556 - 255
12LYSLYSLYSLYS(chain A and (resid 6 through 255 or (resid 256...AA256256
13ALAALAP1TP1T(chain A and (resid 6 through 255 or (resid 256...AA - G6 - 6016
14ALAALAP1TP1T(chain A and (resid 6 through 255 or (resid 256...AA - G6 - 6016
15ALAALAP1TP1T(chain A and (resid 6 through 255 or (resid 256...AA - G6 - 6016
16ALAALAP1TP1T(chain A and (resid 6 through 255 or (resid 256...AA - G6 - 6016
21ALAALAARGARG(chain B and (resid 6 through 255 or (resid 256...BB6 - 2556 - 255
22LYSLYSLYSLYS(chain B and (resid 6 through 255 or (resid 256...BB256256
23ALAALAP1TP1T(chain B and (resid 6 through 255 or (resid 256...BB - H6 - 6016
24ALAALAP1TP1T(chain B and (resid 6 through 255 or (resid 256...BB - H6 - 6016
25ALAALAP1TP1T(chain B and (resid 6 through 255 or (resid 256...BB - H6 - 6016
26ALAALAP1TP1T(chain B and (resid 6 through 255 or (resid 256...BB - H6 - 6016
31ALAALAARGARG(chain C and (resid 6 through 255 or (resid 256...CC6 - 2556 - 255
32LYSLYSLYSLYS(chain C and (resid 6 through 255 or (resid 256...CC256256
33ALAALAP1TP1T(chain C and (resid 6 through 255 or (resid 256...CC - I6 - 6016
41ALAALAARGARG(chain D and (resid 6 through 255 or (resid 256...DD6 - 2556 - 255
42LYSLYSLYSLYS(chain D and (resid 6 through 255 or (resid 256...DD256256
43ALAALAP1TP1T(chain D and (resid 6 through 255 or (resid 256...DD - J6 - 6016
51ALAALAGLYGLY(chain E and (resid 6 through 362 or resid 369...EE6 - 3626 - 362
52PHEPHEGLUGLU(chain E and (resid 6 through 362 or resid 369...EE369 - 385369 - 385
53THRTHRLYSLYS(chain E and (resid 6 through 362 or resid 369...EE386 - 387386 - 387
54ALAALAP1TP1T(chain E and (resid 6 through 362 or resid 369...EE - K6 - 6016
55ALAALAP1TP1T(chain E and (resid 6 through 362 or resid 369...EE - K6 - 6016
56ALAALAP1TP1T(chain E and (resid 6 through 362 or resid 369...EE - K6 - 6016
57ALAALAP1TP1T(chain E and (resid 6 through 362 or resid 369...EE - K6 - 6016
61ALAALAARGARG(chain F and (resid 6 through 255 or (resid 256...FF6 - 2556 - 255
62LYSLYSLYSLYS(chain F and (resid 6 through 255 or (resid 256...FF256256
63ALAALAP1TP1T(chain F and (resid 6 through 255 or (resid 256...FF - L6 - 6016
64ALAALAP1TP1T(chain F and (resid 6 through 255 or (resid 256...FF - L6 - 6016
65ALAALAP1TP1T(chain F and (resid 6 through 255 or (resid 256...FF - L6 - 6016
66ALAALAP1TP1T(chain F and (resid 6 through 255 or (resid 256...FF - L6 - 6016

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Components

#1: Protein
Cystathionine beta-synthase


Mass: 55958.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii 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.: 6 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 7% PEG 3350, 0.1M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→46.81 Å / Num. obs: 55218 / % possible obs: 99.7 % / Redundancy: 8.2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.121 / Rrim(I) all: 0.345 / Net I/σ(I): 8.7 / Num. measured all: 454379 / Scaling rejects: 12625
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
3.15-3.248.42.1363781645180.6810.7832.277299.7
13.37-46.8170.05850837220.9960.0230.06319.797.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBQ

1jbq


Resolution: 3.151→41.025 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2945 1970 3.58 %
Rwork0.2744 52983 -
obs0.2751 54953 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.24 Å2 / Biso mean: 86.6932 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.151→41.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21356 0 126 0 21482
Biso mean--69.07 --
Num. residues----2833
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8424X-RAY DIFFRACTION6.057TORSIONAL
12B8424X-RAY DIFFRACTION6.057TORSIONAL
13C8424X-RAY DIFFRACTION6.057TORSIONAL
14D8424X-RAY DIFFRACTION6.057TORSIONAL
15E8424X-RAY DIFFRACTION6.057TORSIONAL
16F8424X-RAY DIFFRACTION6.057TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1514-3.23020.42951400.41493769100
3.2302-3.31750.44911340.37143862100
3.3175-3.41510.37291430.35953793100
3.4151-3.52520.36111480.34893740100
3.5252-3.65120.33321440.3463777100
3.6512-3.79720.3411370.3146383699
3.7972-3.96990.34071470.3089379099
3.9699-4.1790.32751310.2903373399
4.179-4.44060.30171460.285377299
4.4406-4.7830.29891440.2627377699
4.783-5.26340.29141380.26393768100
5.2634-6.0230.26471480.27413793100
6.023-7.58050.30441410.24533828100
7.5805-41.0250.17171290.176374698
Refinement TLS params.Method: refined / Origin x: -4.0215 Å / Origin y: 13.3361 Å / Origin z: 45.0282 Å
111213212223313233
T0.7625 Å20.1196 Å20.003 Å2-0.615 Å20.0465 Å2--0.7423 Å2
L0.1579 °20.0246 °20.0239 °2-0.1299 °20.0911 °2--0.5296 °2
S-0.0367 Å °0.007 Å °0.0305 Å °0.0796 Å °0.0109 Å °0.0715 Å °0.2042 Å °0.0473 Å °0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 601
2X-RAY DIFFRACTION1allB6 - 601
3X-RAY DIFFRACTION1allC6 - 601
4X-RAY DIFFRACTION1allD6 - 601
5X-RAY DIFFRACTION1allE6 - 601
6X-RAY DIFFRACTION1allF6 - 601

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