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- PDB-6zs7: Crystal structure of delta466-491 cystathionine beta-synthase fro... -

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Basic information

Entry
Database: PDB / ID: 6zs7
TitleCrystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with L-cysteine
ComponentsCystathionine beta-synthase
KeywordsCYTOSOLIC PROTEIN / Transulfuration / hydrogen sulfide / L-cysteine / CBS
Function / homology
Function and homology information


cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / 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. / : / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / 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. / : / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / 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: 3.5 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
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
C: 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
D: Cystathionine beta-synthase
A: 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 area8830 Å2
ΔGint-45 kcal/mol
Surface area35430 Å2
MethodPISA
2
B: 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 area8710 Å2
ΔGint-42 kcal/mol
Surface area35250 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 area8730 Å2
ΔGint-43 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.302, 82.302, 415.980
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 347 or (resid 348...
21(chain B and (resid 6 through 302 or (resid 303...
31(chain C and (resid 6 through 302 or (resid 303...
41(chain D and (resid 6 through 347 or (resid 348...
51(chain E and (resid 6 through 302 or (resid 303...
61(chain F and (resid 6 through 302 or (resid 303...

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
11ALAALALYSLYS(chain A and (resid 6 through 347 or (resid 348...AB6 - 3476 - 347
12GLNGLNGLNGLN(chain A and (resid 6 through 347 or (resid 348...AB348348
13ALAALAP1TP1T(chain A and (resid 6 through 347 or (resid 348...AB - H6 - 6016
21ALAALALEULEU(chain B and (resid 6 through 302 or (resid 303...BC6 - 3026 - 302
22LYSLYSLYSLYS(chain B and (resid 6 through 302 or (resid 303...BC303303
23ALAALAP1TP1T(chain B and (resid 6 through 302 or (resid 303...BC - I6 - 6016
24ALAALAP1TP1T(chain B and (resid 6 through 302 or (resid 303...BC - I6 - 6016
25ALAALAP1TP1T(chain B and (resid 6 through 302 or (resid 303...BC - I6 - 6016
26ALAALAP1TP1T(chain B and (resid 6 through 302 or (resid 303...BC - I6 - 6016
31ALAALALEULEU(chain C and (resid 6 through 302 or (resid 303...CD6 - 3026 - 302
32LYSLYSLYSLYS(chain C and (resid 6 through 302 or (resid 303...CD303303
33ALAALALYSLYS(chain C and (resid 6 through 302 or (resid 303...CD6 - 5126 - 512
34ALAALALYSLYS(chain C and (resid 6 through 302 or (resid 303...CD6 - 5126 - 512
35ALAALALYSLYS(chain C and (resid 6 through 302 or (resid 303...CD6 - 5126 - 512
36ALAALALYSLYS(chain C and (resid 6 through 302 or (resid 303...CD6 - 5126 - 512
41ALAALALYSLYS(chain D and (resid 6 through 347 or (resid 348...DA6 - 3476 - 347
42GLNGLNGLNGLN(chain D and (resid 6 through 347 or (resid 348...DA348348
43ALAALAP1TP1T(chain D and (resid 6 through 347 or (resid 348...DA - G6 - 6016
44ALAALAP1TP1T(chain D and (resid 6 through 347 or (resid 348...DA - G6 - 6016
45ALAALAP1TP1T(chain D and (resid 6 through 347 or (resid 348...DA - G6 - 6016
46ALAALAP1TP1T(chain D and (resid 6 through 347 or (resid 348...DA - G6 - 6016
51ALAALALEULEU(chain E and (resid 6 through 302 or (resid 303...EE6 - 3026 - 302
52LYSLYSLYSLYS(chain E and (resid 6 through 302 or (resid 303...EE303303
53ALAALALYSLYS(chain E and (resid 6 through 302 or (resid 303...EE6 - 5126 - 512
54ALAALALYSLYS(chain E and (resid 6 through 302 or (resid 303...EE6 - 5126 - 512
55ALAALALYSLYS(chain E and (resid 6 through 302 or (resid 303...EE6 - 5126 - 512
56ALAALALYSLYS(chain E and (resid 6 through 302 or (resid 303...EE6 - 5126 - 512
61ALAALALEULEU(chain F and (resid 6 through 302 or (resid 303...FF6 - 3026 - 302
62LYSLYSLYSLYS(chain F and (resid 6 through 302 or (resid 303...FF303303
63ALAALAP1TP1T(chain F and (resid 6 through 302 or (resid 303...FF - L6 - 6016
64ALAALAP1TP1T(chain F and (resid 6 through 302 or (resid 303...FF - L6 - 6016
65ALAALAP1TP1T(chain F and (resid 6 through 302 or (resid 303...FF - L6 - 6016
66ALAALAP1TP1T(chain F and (resid 6 through 302 or (resid 303...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 (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / 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: 2.61 Å3/Da / Density % sol: 51.79 %
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: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.178→138.66 Å / Num. obs: 46649 / % possible obs: 91 % / Redundancy: 10.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.367 / Rpim(I) all: 0.125 / Rrim(I) all: 0.389 / Net I/σ(I): 10.4 / Num. measured all: 472238
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
3.178-3.36910.92.1272545323310.4110.6752.2321.434.7
8.982-138.669.70.0612256223320.9960.020.06427.899.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.18phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBQ

1jbq


Resolution: 3.5→67.43 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 1981 5 %
Rwork0.2713 37632 -
obs0.2718 39613 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.47 Å2 / Biso mean: 61.3415 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.5→67.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20980 0 126 0 21106
Biso mean--42.16 --
Num. residues----2802
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8172X-RAY DIFFRACTION4.37TORSIONAL
12B8172X-RAY DIFFRACTION4.37TORSIONAL
13C8172X-RAY DIFFRACTION4.37TORSIONAL
14D8172X-RAY DIFFRACTION4.37TORSIONAL
15E8172X-RAY DIFFRACTION4.37TORSIONAL
16F8172X-RAY DIFFRACTION4.37TORSIONAL
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 (%)
3.5-3.590.34621460.354327342880100
3.59-3.680.39361350.323226512786100
3.68-3.790.36191520.315526872839100
3.79-3.920.32421480.327827192867100
3.92-4.060.36641400.300326652805100
4.06-4.220.29441350.293626602795100
4.22-4.410.28111390.2882665280499
4.41-4.640.24581380.267827492887100
4.64-4.930.24591450.261626942839100
4.93-5.310.30421380.268426592797100
5.31-5.850.30051430.26627192862100
5.85-6.690.25071320.274926762808100
6.69-8.430.24911400.208227162856100
8.43-67.430.18631500.19212638278898
Refinement TLS params.Method: refined / Origin x: 66.3709 Å / Origin y: -20.1469 Å / Origin z: 44.8255 Å
111213212223313233
T0.3673 Å2-0.0463 Å2-0.0259 Å2-0.3572 Å2-0.0005 Å2--0.4838 Å2
L0.0764 °2-0.0768 °2-0.043 °2-0.0839 °20.1627 °2--0.5269 °2
S-0.0596 Å °-0.08 Å °0.0626 Å °-0.0863 Å °-0.0429 Å °0.0585 Å °-0.1562 Å °-0.0297 Å °0.0956 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
4X-RAY DIFFRACTION1allC6 - 512
5X-RAY DIFFRACTION1allC601
6X-RAY DIFFRACTION1allE6 - 512
7X-RAY DIFFRACTION1allE601
8X-RAY DIFFRACTION1allF6 - 601

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