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- PDB-3fpz: Saccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase -

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Basic information

Entry
Database: PDB / ID: 3fpz
TitleSaccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase
ComponentsThiazole biosynthetic enzyme
KeywordsBIOSYNTHETIC PROTEIN / Thiazole biosynthetic enzyme in yeast / FAD / Mitochondrion / NAD / Thiamine biosynthesis / Transit peptide
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-AHZ / Thiamine thiazole synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å
AuthorsBale, S. / Chatterjee, A. / Dorrestein, P.C. / Begley, T.P. / Ealick, S.E.
Citation
Journal: Nature / Year: 2011
Title: Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase.
Authors: Chatterjee, A. / Abeydeera, N.D. / Bale, S. / Pai, P.J. / Dorrestein, P.C. / Russell, D.H. / Ealick, S.E. / Begley, T.P.
#1: Journal: Biochemistry / Year: 2006
Title: Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae.
Authors: Jurgenson, C.T. / Chatterjee, A. / Begley, T.P. / Ealick, S.E.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJan 19, 2010ID: 2GJC
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiazole biosynthetic enzyme
B: Thiazole biosynthetic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4677
Polymers69,9922
Non-polymers1,4755
Water8,845491
1
A: Thiazole biosynthetic enzyme
B: Thiazole biosynthetic enzyme
hetero molecules

A: Thiazole biosynthetic enzyme
B: Thiazole biosynthetic enzyme
hetero molecules

A: Thiazole biosynthetic enzyme
B: Thiazole biosynthetic enzyme
hetero molecules

A: Thiazole biosynthetic enzyme
B: Thiazole biosynthetic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,86628
Polymers279,9668
Non-polymers5,90020
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area60810 Å2
ΔGint-367 kcal/mol
Surface area74210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.696, 140.696, 73.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 16 - 326 / Label seq-ID: 16 - 326

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Thiazole biosynthetic enzyme / Yeast Thiazole synthase


Mass: 34995.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THI4, ESP35, MOL1, YGR144W, G6620 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P32318
#2: Chemical ChemComp-AHZ / ADENOSINE DIPHOSPHATE 5-(BETA-ETHYL)-4-METHYL-THIAZOLE-2-CARBOXYLIC ACID


Mass: 593.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N6O12P2S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE FORMATION OF DHA FROM CYS IS DUE TO THE REACTION CATALYZED BY THE ENZYME.

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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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.65-2.00 M Li2SO4, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9831 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9831 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 63286 / Num. obs: 63274 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Χ2: 0.96 / Net I/σ(I): 22.669
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6023 / Rsym value: 0.256 / Χ2: 0.803 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
CNSphasing
RefinementStarting model: PDB entry 1RP0

1rp0


Resolution: 1.82→49.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.694 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3212 5.1 %RANDOM
Rwork0.195 ---
all0.198 63286 --
obs0.198 63274 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.97 Å2 / Biso mean: 28.26 Å2 / Biso min: 12.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.82→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 91 491 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224848
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9776599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45624.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78315768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1671518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213636
X-RAY DIFFRACTIONr_mcbond_it0.7851.53076
X-RAY DIFFRACTIONr_mcangle_it1.42824929
X-RAY DIFFRACTIONr_scbond_it1.74731772
X-RAY DIFFRACTIONr_scangle_it2.7794.51668
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2306 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.395
BLOOSE THERMAL0.8310
LS refinement shellResolution: 1.822→1.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 228 -
Rwork0.249 4248 -
all-4476 -
obs-6023 95.34 %

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