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- PDB-4s25: Crystal structure of Arabidopsis thaliana ThiC with bound imidazo... -

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Basic information

Entry
Database: PDB / ID: 4s25
TitleCrystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Zn (trigonal 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
1,4-BUTANEDIOL / Chem-IRN / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Phosphomethylpyrimidine synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 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_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_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_label_atom_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9678
Polymers64,6701
Non-polymers1,2977
Water9,350519
1
A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules

A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,93516
Polymers129,3402
Non-polymers2,59514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10780 Å2
ΔGint-225 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.477, 107.477, 87.643
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1210-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / 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 , 7 types, 526 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na acetate, pH5.3-5.6, 1-9%(v/v) 1,4 butanediol, pH 5.5, 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: 1.45→50 Å / Num. all: 100732 / Num. obs: 100712 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 10.53 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.45-1.54.60.435199.2
1.5-1.564.60.322198.9
1.56-1.634.60.241198.8
1.63-1.724.90.191198.4
1.72-1.834.80.141198.2
1.83-1.974.70.102197.7
1.97-2.175.10.075197
2.17-2.484.80.056196.4
2.48-3.125.30.046195.3
3.12-505.10.033192.2

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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: FOURIER SYNTHESIS
Starting model: PDB entry 4N7Q

4n7q


Resolution: 1.45→46.539 Å / SU ML: 0.11 / σ(F): 1.39 / Phase error: 14.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 4973 4.94 %
Rwork0.1425 --
obs0.1435 100712 97.1 %
all-100732 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.237 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 66 519 4640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074511
X-RAY DIFFRACTIONf_angle_d1.1736154
X-RAY DIFFRACTIONf_dihedral_angle_d13.4091683
X-RAY DIFFRACTIONf_chiral_restr0.079655
X-RAY DIFFRACTIONf_plane_restr0.006807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46520.23371760.20333135X-RAY DIFFRACTION96
1.4652-1.48250.20321720.18653190X-RAY DIFFRACTION99
1.4825-1.50050.21211490.17793258X-RAY DIFFRACTION99
1.5005-1.51950.19132030.16053214X-RAY DIFFRACTION99
1.5195-1.53950.18161560.1633237X-RAY DIFFRACTION99
1.5395-1.56060.20641470.15363248X-RAY DIFFRACTION99
1.5606-1.58290.16731600.15473238X-RAY DIFFRACTION99
1.5829-1.60660.16971310.14993250X-RAY DIFFRACTION99
1.6066-1.63170.16961570.14073217X-RAY DIFFRACTION98
1.6317-1.65840.171740.1433181X-RAY DIFFRACTION98
1.6584-1.6870.19251440.14443257X-RAY DIFFRACTION98
1.687-1.71770.1541700.1393182X-RAY DIFFRACTION98
1.7177-1.75070.17781890.13983200X-RAY DIFFRACTION98
1.7507-1.78650.18061690.13993220X-RAY DIFFRACTION98
1.7865-1.82530.18581620.14613235X-RAY DIFFRACTION98
1.8253-1.86780.16381480.14213202X-RAY DIFFRACTION98
1.8678-1.91450.17051740.14213146X-RAY DIFFRACTION98
1.9145-1.96620.14291900.13563180X-RAY DIFFRACTION98
1.9662-2.02410.16751680.13453218X-RAY DIFFRACTION97
2.0241-2.08940.1541760.13093161X-RAY DIFFRACTION97
2.0894-2.16410.15761480.13973188X-RAY DIFFRACTION97
2.1641-2.25080.15371350.13543218X-RAY DIFFRACTION97
2.2508-2.35320.15251570.13753183X-RAY DIFFRACTION97
2.3532-2.47720.17411700.13933182X-RAY DIFFRACTION96
2.4772-2.63240.15161940.13873122X-RAY DIFFRACTION96
2.6324-2.83570.15931750.14643153X-RAY DIFFRACTION95
2.8357-3.1210.16041900.14233113X-RAY DIFFRACTION95
3.121-3.57250.14521610.14113137X-RAY DIFFRACTION94
3.5725-4.50030.1531710.13173125X-RAY DIFFRACTION93
4.5003-46.56290.13911570.14313149X-RAY DIFFRACTION90

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