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- PDB-4y4l: Crystal structure of yeast Thi4-C205S -

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Basic information

Entry
Database: PDB / ID: 4y4l
TitleCrystal structure of yeast Thi4-C205S
ComponentsThiamine thiazole synthase
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


cysteine-dependent adenosine diphosphate thiazole synthase / thiazole biosynthetic process / pentosyltransferase activity / thiamine biosynthetic process / mitochondrial genome maintenance / ferrous iron binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2840 / Thiamine thiazole synthase / Thi4 family / Thiazole biosynthetic enzyme Thi4 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2840 / Thiamine thiazole synthase / Thi4 family / Thiazole biosynthetic enzyme Thi4 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-48N / Thiamine thiazole synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, X. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases.
Authors: Zhang, X. / Eser, B.E. / Chanani, P.K. / Begley, T.P. / Ealick, S.E.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,1348
Polymers148,7414
Non-polymers2,3934
Water5,999333
1
A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
hetero molecules

A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
hetero molecules

A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
hetero molecules

A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,26816
Polymers297,4818
Non-polymers4,7878
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation3_745-y+2,x-1,z1
crystal symmetry operation4_675y+1,-x+2,z1
Buried area58700 Å2
ΔGint-371 kcal/mol
Surface area65950 Å2
MethodPISA
2
C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules

C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules

C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules

C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,26816
Polymers297,4818
Non-polymers4,7878
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area58040 Å2
ΔGint-350 kcal/mol
Surface area66070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.393, 127.393, 72.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Thiamine thiazole synthase / Thiazole biosynthetic enzyme


Mass: 37185.180 Da / Num. of mol.: 4 / Mutation: C205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: THI4, ESP35, MOL1, YGR144W, G6620 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P32318
#2: Chemical
ChemComp-48N / (2E)-2-[(2S,4R)-5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-3-oxidanylidene-pentan-2-yl]iminoethanoic acid


Mass: 598.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H24N6O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 8.5
Details: 25% (w/v) PEG1500, 0.0125 M succinic acid, 0.04375M sodium dihydrogen phosphate, and 0.04375M glycine, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 78765 / % possible obs: 100 % / Redundancy: 5 % / Rsym value: 0.07 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FPZ

3fpz


Resolution: 2→38.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19224 3955 5 %RANDOM
Rwork0.17092 ---
obs0.17198 74670 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 156 333 9569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0229502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9712908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78951215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5724.43377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.141151547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7331537
X-RAY DIFFRACTIONr_chiral_restr0.0620.21474
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9171.55989
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61829618
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.86133513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4554.53285
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 274 -
Rwork0.202 5409 -
obs--98.29 %

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