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- PDB-6hk1: Crystal structure of the Thiazole synthase from Methanothermococc... -

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Basic information

Entry
Database: PDB / ID: 6hk1
TitleCrystal structure of the Thiazole synthase from Methanothermococcus thermolithotrophicus co-crystallized with Tb-Xo4
ComponentsThiazole synthase
KeywordsBIOSYNTHETIC PROTEIN / native purification / de novo phasing / nucleating agent / crystallophore / Tb-Xo4 / Lanthanide complex / molecular glue
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 / Thi4 family / Thiazole biosynthetic enzyme Thi4 family / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-48F / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TERBIUM(III) ION / Thiamine thiazole synthase
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsEngilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
Funding support France, Germany, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 France
Max Planck Society Germany
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: Protein crystal structure determination with the crystallophore, a nucleating and phasing agent.
Authors: Engilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
History
DepositionSep 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiazole synthase
B: Thiazole synthase
C: Thiazole synthase
D: Thiazole synthase
E: Thiazole synthase
F: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,44068
Polymers167,5336
Non-polymers11,90762
Water7,728429
1
A: Thiazole synthase
E: Thiazole synthase
hetero molecules

A: Thiazole synthase
E: Thiazole synthase
hetero molecules

A: Thiazole synthase
E: Thiazole synthase
hetero molecules

A: Thiazole synthase
E: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,135124
Polymers223,3788
Non-polymers20,757116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area48670 Å2
ΔGint-369 kcal/mol
Surface area64070 Å2
MethodPISA
2
B: Thiazole synthase
C: Thiazole synthase
D: Thiazole synthase
F: Thiazole synthase
hetero molecules

B: Thiazole synthase
C: Thiazole synthase
D: Thiazole synthase
F: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,81374
Polymers223,3788
Non-polymers13,43566
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area45060 Å2
ΔGint-326 kcal/mol
Surface area63070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.863, 216.863, 207.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Thiazole synthase /


Mass: 27922.209 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus (archaea)
References: UniProt: A0A5H1ZR31*PLUS

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Non-polymers , 7 types, 491 molecules

#2: Chemical...
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: Tb
#3: Chemical
ChemComp-48F / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 44 % PEE 797, 100 mM HEPES pH 8.0, 10 mM TbXo4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.64 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.64 Å / Relative weight: 1
ReflectionResolution: 2.55→49.09 Å / Num. obs: 79226 / % possible obs: 98.9 % / Redundancy: 39.8 % / Biso Wilson estimate: 68.14 Å2 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.054 / Net I/σ(I): 14.6
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.6 / Rpim(I) all: 0.46 / % possible all: 94.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→49.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3959 5 %RANDOM
Rwork0.189 ---
obs0.19 79226 98.8 %-
Displacement parametersBiso mean: 55.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.1668 Å20 Å20 Å2
2--2.1668 Å20 Å2
3----4.3336 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.55→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11652 0 330 438 12420
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00523979HARMONIC6
X-RAY DIFFRACTIONt_angle_deg0.9243485HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d5489SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3671HARMONIC30
X-RAY DIFFRACTIONt_it23979HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.7
X-RAY DIFFRACTIONt_other_torsion15.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1574SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25665SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2671 264 4.94 %
Rwork0.2544 5080 -
all0.255 5344 -
obs--91.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1090.078-0.11930.4077-0.14030.2742-0.00740.02730.0486-0.0389-0.00450.09220.0234-0.06640.0119-0.04860.0309-0.022-0.03580.013-0.0455-21.947217.543337.6661
20.1384-0.1419-0.03250.476-0.1930.2687-0.0230.06890.0273-0.047-0.0201-0.0695-0.0380.06410.043-0.0797-0.11450.0009-0.03840.0696-0.0569-43.1172-45.996375.926
30.48840.1210.26090.3233-0.12830.34140.0115-0.00540.05860.0482-0.00980.0675-0.0565-0.1133-0.0017-0.0668-0.0184-0.01-0.0793-0.0237-0.0162-83.0808-44.097108.863
40.5136-0.26420.02410.89830.28980.3864-0.03650.12060.0024-0.0502-0.03350.02-0.03930.01060.07-0.0687-0.0928-0.0188-0.04320.0194-0.0826-67.0844-59.389976.1967
50.1209-0.1098-0.01650.4787-0.180.2427-0.0108-0.0393-0.05110.04710.00780.05760.0176-0.05360.0031-0.0671-0.02830.0218-0.04640.0122-0.0351-22.6957-16.591163.5994
60.27080.0895-0.00810.41020.06750.4691-0.0180.06870.09080.0084-0.01030.0122-0.13380.0020.02830.0084-0.0552-0.0707-0.16910.0246-0.0244-64.6289-24.8988101.613
70.32040.3251-0.34320.3612-0.48150.28760.0030.02010.0259-0.0163-0.0138-0.0211-0.0239-0.01680.0108-0.0082-0.03830.016-0.02620.0273-0.0145-46.7808-30.307178.994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ H|* }

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