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- PDB-6z3s: Crystal structure of delta466-491 cystathionine beta-synthase fro... -

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Basic information

Entry
Database: PDB / ID: 6z3s
TitleCrystal structure of delta466-491 cystathionine beta-synthase from Toxoplasma gondii with O-Acetylserine
ComponentsCystathionine beta-synthase
KeywordsCYTOSOLIC PROTEIN / Transulfuration / hydrogen sulfide / O-acetylserine / 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 ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.048 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
DepositionMay 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)161,1086
Polymers160,1533
Non-polymers9553
Water00
1
D: Cystathionine beta-synthase
hetero molecules

D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4054
Polymers106,7692
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8700 Å2
ΔGint-48 kcal/mol
Surface area35680 Å2
MethodPISA
2
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4054
Polymers106,7692
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-43 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.700, 82.700, 422.968
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 363 or (resid 364...
21(chain B and (resid 6 through 397 or resid 405 through 601))
31(chain D and (resid 6 through 462 or resid 496 through 601))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 363 or (resid 364...A6 - 363
121(chain A and (resid 6 through 363 or (resid 364...A364 - 366
131(chain A and (resid 6 through 363 or (resid 364...A6 - 601
141(chain A and (resid 6 through 363 or (resid 364...A6 - 601
151(chain A and (resid 6 through 363 or (resid 364...A6 - 601
161(chain A and (resid 6 through 363 or (resid 364...A6 - 601
211(chain B and (resid 6 through 397 or resid 405 through 601))B6 - 397
221(chain B and (resid 6 through 397 or resid 405 through 601))B405 - 601
311(chain D and (resid 6 through 462 or resid 496 through 601))D6 - 462
321(chain D and (resid 6 through 462 or resid 496 through 601))D496 - 601

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Components

#1: Protein Cystathionine beta-synthase


Mass: 53384.320 Da / Num. of mol.: 3
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.: 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.1 / Details: 10% 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 PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.048→140.989 Å / Num. obs: 26412 / % possible obs: 90.1 % / Redundancy: 16.8 % / CC1/2: 0.969 / Rmerge(I) obs: 0.719 / Rpim(I) all: 0.178 / Rrim(I) all: 0.742 / Net I/σ(I): 8.6
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
3.065-3.32513.411.7141776413220.6383.18212.1661.638.3
9.363-140.98913.20.121736913200.9950.0320.12518.799.3

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Processing

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

1jbq


Resolution: 3.048→70.615 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1308 4.96 %
Rwork0.2678 25066 -
obs0.2688 26374 79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.29 Å2 / Biso mean: 68.6063 Å2 / Biso min: 39.9 Å2
Refinement stepCycle: final / Resolution: 3.048→70.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 63 0 10623
Biso mean--49.43 --
Num. residues----1405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4275X-RAY DIFFRACTION0.925TORSIONAL
12B4275X-RAY DIFFRACTION0.925TORSIONAL
13D4275X-RAY DIFFRACTION0.925TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.048-3.16990.3536110.42652507
3.1699-3.31410.3724610.360590727
3.3141-3.48880.35091270.3389256775
3.4888-3.70740.38341850.32063449100
3.7074-3.99360.34951850.30583496100
3.9936-4.39550.30241910.2733483100
4.3955-5.03140.26911610.2493527100
5.0314-6.33840.29541810.26473620100
6.3384-70.6150.21082060.2165376799
Refinement TLS params.Method: refined / Origin x: 14.4408 Å / Origin y: -13.3751 Å / Origin z: -33.5611 Å
111213212223313233
T0.2428 Å20.0534 Å2-0.0997 Å2-0.7157 Å20.0282 Å2--0.5684 Å2
L-0.1879 °2-0.0463 °2-0.2401 °2-0.8538 °20.5438 °2--0.8394 °2
S-0.0762 Å °-0.0419 Å °-0.0175 Å °-0.0167 Å °0.002 Å °-0.0005 Å °0.0788 Å °-0.1152 Å °0.0604 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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