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- PDB-4s26: Crystal structure of Arabidopsis thaliana ThiC with bound imidazo... -

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Basic information

Entry
Database: PDB / ID: 4s26
TitleCrystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Zn (monoclinic crystal form)
ComponentsPhosphomethylpyrimidine synthase, chloroplastic
KeywordsLYASE / Alpha-Beta Barrel / Radical SAM superfamily / Iron-sulfur cluster / Thiamin / Vitamin B1 / Vitamin B12 / Domain swapping / AdoMet and Glutamate mutase
Function / homology
Function and homology information


phosphomethylpyrimidine synthase / response to vitamin B1 / carbon-carbon lyase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / chloroplast stroma / plastid / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding ...phosphomethylpyrimidine synthase / response to vitamin B1 / carbon-carbon lyase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / chloroplast stroma / plastid / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding / protein domain specific binding / metal ion binding
Similarity search - Function
Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-IRN / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Phosphomethylpyrimidine synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E.
CitationJournal: Nat Commun
Title: Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Authors: Fenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S.H. / Begley, T.P. / Ealick, S.E.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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.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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Phosphomethylpyrimidine synthase, chloroplastic
B: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,57412
Polymers129,3402
Non-polymers2,23410
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-235 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.911, 95.596, 71.414
Angle α, β, γ (deg.)90.00, 104.22, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and resseq 104:109
21chain B and resseq 104:109
12chain A and resseq 157:162
22chain B and resseq 157:162
13chain A and resseq 202:212
23chain B and resseq 202:212
14chain A and resseq 234:238
24chain B and resseq 234:238
15chain A and resseq 259:261
25chain B and resseq 259:261
16chain A and resseq 319:325
26chain B and resseq 319:325
17chain A and resseq 560:595
27chain B and resseq 560:595

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHISchain A and resseq 104:109AA104 - 10936 - 41
21HISHISHISHISchain B and resseq 104:109BB104 - 10936 - 41
12LYSLYSARGARGchain A and resseq 157:162AA157 - 16289 - 94
22LYSLYSARGARGchain B and resseq 157:162BB157 - 16289 - 94
13ILEILELEULEUchain A and resseq 202:212AA202 - 212134 - 144
23ILEILELEULEUchain B and resseq 202:212BB202 - 212134 - 144
14VALVALILEILEchain A and resseq 234:238AA234 - 238166 - 170
24VALVALILEILEchain B and resseq 234:238BB234 - 238166 - 170
15LEULEUTHRTHRchain A and resseq 259:261AA259 - 261191 - 193
25LEULEUTHRTHRchain B and resseq 259:261BB259 - 261191 - 193
16PHEPHEVALVALchain A and resseq 319:325AA319 - 325251 - 257
26PHEPHEVALVALchain B and resseq 319:325BB319 - 325251 - 257
17PROPROTYRTYRchain A and resseq 560:595AA560 - 595492 - 527
27PROPROTYRTYRchain B and resseq 560:595BB560 - 595492 - 527

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphomethylpyrimidine synthase, chloroplastic / Hydroxymethylpyrimidine phosphate synthase / HMP-P synthase / HMP-phosphate synthase / HMPP ...Hydroxymethylpyrimidine phosphate synthase / HMP-P synthase / HMP-phosphate synthase / HMPP synthase / Protein PYRIMIDINE REQUIRING / Thiamine biosynthesis protein ThiC / Protein THIAMINE C


Mass: 64670.090 Da / Num. of mol.: 2 / Fragment: UNP residues 72-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: THIC, PY / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O82392, phosphomethylpyrimidine synthase

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Non-polymers , 6 types, 554 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-IRN / 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole


Type: RNA linking / Mass: 280.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O7P
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100 mM imidazole, pH 6.6, 200 mM NaCl, and 20% (w/v) polyethylene glycol (PEG) 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 94824 / Num. obs: 94814 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.922.50.462197.1
1.92-1.992.80.324198.3
1.99-2.082.90.237198.5
2.08-2.192.80.177198.3
2.19-2.332.60.133197.3
2.33-2.512.90.105198.4
2.51-2.762.90.083197.4
2.76-3.162.80.065196.3
3.16-3.9930.047195.7
3.99-5030.039191.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_1839refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N7Q

4n7q


Resolution: 1.85→48.256 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 4595 4.85 %
Rwork0.1673 --
obs0.1688 94814 96.08 %
all-94824 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7902 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 108 544 8721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088425
X-RAY DIFFRACTIONf_angle_d1.07411464
X-RAY DIFFRACTIONf_dihedral_angle_d13.653057
X-RAY DIFFRACTIONf_chiral_restr0.0451246
X-RAY DIFFRACTIONf_plane_restr0.0051474
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A40X-RAY DIFFRACTIONPOSITIONAL0.044
12B40X-RAY DIFFRACTIONPOSITIONAL0.044
21A39X-RAY DIFFRACTIONPOSITIONAL0.021
22B39X-RAY DIFFRACTIONPOSITIONAL0.021
31A90X-RAY DIFFRACTIONPOSITIONAL0.063
32B90X-RAY DIFFRACTIONPOSITIONAL0.063
41A32X-RAY DIFFRACTIONPOSITIONAL0.047
42B32X-RAY DIFFRACTIONPOSITIONAL0.047
51A21X-RAY DIFFRACTIONPOSITIONAL0.051
52B21X-RAY DIFFRACTIONPOSITIONAL0.051
61A52X-RAY DIFFRACTIONPOSITIONAL0.053
62B52X-RAY DIFFRACTIONPOSITIONAL0.053
71A245X-RAY DIFFRACTIONPOSITIONAL0.079
72B245X-RAY DIFFRACTIONPOSITIONAL0.079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.86470.29751160.25542306X-RAY DIFFRACTION74
1.8647-1.88660.28951610.23563042X-RAY DIFFRACTION97
1.8866-1.90960.2491410.22393000X-RAY DIFFRACTION97
1.9096-1.93380.251550.21523027X-RAY DIFFRACTION97
1.9338-1.95930.22221350.20083127X-RAY DIFFRACTION99
1.9593-1.98610.22181760.1953042X-RAY DIFFRACTION99
1.9861-2.01450.21661390.19293079X-RAY DIFFRACTION99
2.0145-2.04450.25571500.19673116X-RAY DIFFRACTION99
2.0445-2.07650.25291620.1913065X-RAY DIFFRACTION98
2.0765-2.11050.23861680.19323046X-RAY DIFFRACTION98
2.1105-2.14690.23641770.19443025X-RAY DIFFRACTION98
2.1469-2.1860.23811650.18983037X-RAY DIFFRACTION98
2.186-2.2280.2251680.18073081X-RAY DIFFRACTION98
2.228-2.27350.21591490.17773056X-RAY DIFFRACTION97
2.2735-2.32290.20441410.17143025X-RAY DIFFRACTION96
2.3229-2.3770.21441300.17333081X-RAY DIFFRACTION98
2.377-2.43640.18421560.17323100X-RAY DIFFRACTION99
2.4364-2.50230.23981720.17383043X-RAY DIFFRACTION98
2.5023-2.57590.22051430.17013054X-RAY DIFFRACTION98
2.5759-2.6590.24791460.16523062X-RAY DIFFRACTION97
2.659-2.75410.19511690.17333011X-RAY DIFFRACTION97
2.7541-2.86430.23241580.17923065X-RAY DIFFRACTION97
2.8643-2.99470.21721450.17912963X-RAY DIFFRACTION95
2.9947-3.15250.19891560.1773019X-RAY DIFFRACTION97
3.1525-3.350.20151520.1713063X-RAY DIFFRACTION97
3.35-3.60860.171550.16453016X-RAY DIFFRACTION96
3.6086-3.97150.15921500.13632978X-RAY DIFFRACTION94
3.9715-4.54590.14151550.12712882X-RAY DIFFRACTION92
4.5459-5.72580.15481580.13412907X-RAY DIFFRACTION93
5.7258-48.27250.15481470.13982901X-RAY DIFFRACTION90

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