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- PDB-7rk0: Crystal structure of Thermovibrio ammonificans THI4 -

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Basic information

Entry
Database: PDB / ID: 7rk0
TitleCrystal structure of Thermovibrio ammonificans THI4
ComponentsThiamine thiazole synthase
KeywordsBIOSYNTHETIC PROTEIN / suicide enzyme / thiamin / thiazole
Function / homology
Function and homology information


sulfide-dependent adenosine diphosphate thiazole synthase / thiazole biosynthetic process / pentosyltransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / iron ion binding
Similarity search - Function
Thiazole biosynthetic enzyme, prokaryotic / Thiazole biosynthetic enzyme Thi4 family / Thi4 family / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-48H / : / Thiamine thiazole synthase
Similarity search - Component
Biological speciesThermovibrio ammonificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLi, Q. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020153 United States
CitationJournal: Biochem.J. / Year: 2021
Title: Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases.
Authors: Joshi, J. / Li, Q. / Garcia-Garcia, J.D. / Leong, B.J. / Hu, Y. / Bruner, S.D. / Hanson, A.D.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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
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)117,68112
Polymers115,0644
Non-polymers2,6178
Water61334
1
A: Thiamine thiazole synthase
B: Thiamine thiazole synthase
C: Thiamine thiazole synthase
D: Thiamine thiazole synthase
hetero molecules

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)235,36224
Polymers230,1298
Non-polymers5,23416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area45510 Å2
ΔGint-462 kcal/mol
Surface area57600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.889, 89.685, 131.813
Angle α, β, γ (deg.)90.000, 96.979, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein
Thiamine thiazole synthase


Mass: 28766.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermovibrio ammonificans (bacteria) / Gene: thi4, Theam_0077 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E8T346, sulfide-dependent adenosine diphosphate thiazole synthase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-48H / 2-[(E)-[(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-ylidene]amino]ethanoic acid


Mass: 598.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H24N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES-NaOH pH 7.5, 200 mM NaCl, 35% 2-methyl-2,4-pentanediol, 10 mM praseodymium acetate hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.28→44.84 Å / Num. obs: 47059 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 44.41 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.23
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 4604 / CC1/2: 0.125

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4N

4y4n


Resolution: 2.28→44.84 Å / SU ML: 0.429 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 34.7624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2774 2512 5.34 %
Rwork0.2179 44500 -
obs0.2212 47012 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.13 Å2
Refinement stepCycle: LAST / Resolution: 2.28→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7835 0 160 34 8029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00988130
X-RAY DIFFRACTIONf_angle_d1.298811020
X-RAY DIFFRACTIONf_chiral_restr0.06261270
X-RAY DIFFRACTIONf_plane_restr0.00771385
X-RAY DIFFRACTIONf_dihedral_angle_d11.66661134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.330.39991140.35322358X-RAY DIFFRACTION93.92
2.33-2.380.40521460.33862482X-RAY DIFFRACTION99.96
2.38-2.430.38111420.33642458X-RAY DIFFRACTION100
2.43-2.480.38791670.32532438X-RAY DIFFRACTION99.92
2.48-2.550.37191210.32132460X-RAY DIFFRACTION99.88
2.55-2.610.39431690.30362444X-RAY DIFFRACTION99.85
2.61-2.690.33261390.29652476X-RAY DIFFRACTION100
2.69-2.780.34121460.27032460X-RAY DIFFRACTION99.89
2.78-2.880.32061290.25922508X-RAY DIFFRACTION99.85
2.88-2.990.34141110.23492521X-RAY DIFFRACTION99.7
2.99-3.130.32241170.23282473X-RAY DIFFRACTION99.88
3.13-3.290.33611330.21832467X-RAY DIFFRACTION99.81
3.29-3.50.30011440.21362496X-RAY DIFFRACTION99.74
3.5-3.770.26231510.19032454X-RAY DIFFRACTION99.62
3.77-4.150.20651300.17522501X-RAY DIFFRACTION100
4.15-4.750.21841690.15622461X-RAY DIFFRACTION99.73
4.75-5.980.24961450.19172520X-RAY DIFFRACTION99.96
5.98-44.840.22561390.18922523X-RAY DIFFRACTION98.89

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