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- PDB-4s28: Crystal structure of Arabidopsis thaliana ThiC with bound aminoim... -

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Basic information

Entry
Database: PDB / ID: 4s28
TitleCrystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Fe
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
5-AMINOIMIDAZOLE RIBONUCLEOTIDE / 1,4-BUTANEDIOL / : / 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: 1.25 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_alt_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_alt_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.pdbx_ptnr1_label_alt_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_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)65,9738
Polymers64,6701
Non-polymers1,3037
Water9,890549
1
A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules

A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,94616
Polymers129,3402
Non-polymers2,60614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area12770 Å2
ΔGint-169 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.071, 107.071, 87.677
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-1223-

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, 556 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-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE


Mass: 295.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O7P
#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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 549 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
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: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 158608 / Num. obs: 158556 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 9.91 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.25-1.294.50.333196.5
1.29-1.355.40.299198.6
1.35-1.415.30.227199
1.41-1.485.20.167199.1
1.48-1.575.50.125199.3
1.57-1.75.10.092199.3
1.7-1.875.60.072199.6
1.87-2.145.30.051199.7
2.14-2.695.70.042199.9
2.69-505.40.03199.3

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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: 1.25→40.986 Å / SU ML: 0.07 / σ(F): 1.37 / Phase error: 10.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1367 7765 4.9 %
Rwork0.1157 --
obs0.1168 158556 99.04 %
all-158608 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.9927 Å2
Refinement stepCycle: LAST / Resolution: 1.25→40.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 67 549 4720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074593
X-RAY DIFFRACTIONf_angle_d1.2266271
X-RAY DIFFRACTIONf_dihedral_angle_d13.4991704
X-RAY DIFFRACTIONf_chiral_restr0.079666
X-RAY DIFFRACTIONf_plane_restr0.006820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26310.18472360.15584656X-RAY DIFFRACTION92
1.2631-1.27790.1542720.14014928X-RAY DIFFRACTION98
1.2779-1.29350.15262060.12945028X-RAY DIFFRACTION98
1.2935-1.30990.15783000.12564894X-RAY DIFFRACTION98
1.3099-1.32710.16052490.12184964X-RAY DIFFRACTION99
1.3271-1.34530.15642360.11775039X-RAY DIFFRACTION99
1.3453-1.36450.14092540.10814957X-RAY DIFFRACTION99
1.3645-1.38490.12472580.10595005X-RAY DIFFRACTION99
1.3849-1.40650.13772540.10474979X-RAY DIFFRACTION99
1.4065-1.42960.14382450.10615002X-RAY DIFFRACTION99
1.4296-1.45430.12742420.09995020X-RAY DIFFRACTION99
1.4543-1.48070.12262760.10084977X-RAY DIFFRACTION99
1.4807-1.50920.1262670.08925026X-RAY DIFFRACTION99
1.5092-1.540.12562610.08655001X-RAY DIFFRACTION99
1.54-1.57350.11172510.08585047X-RAY DIFFRACTION100
1.5735-1.61010.11512000.08755067X-RAY DIFFRACTION100
1.6101-1.65040.10932650.08975049X-RAY DIFFRACTION99
1.6504-1.6950.12322330.09345026X-RAY DIFFRACTION99
1.695-1.74490.11692880.09264979X-RAY DIFFRACTION99
1.7449-1.80120.12872470.09655080X-RAY DIFFRACTION100
1.8012-1.86550.13032590.1035070X-RAY DIFFRACTION100
1.8655-1.94020.11832960.10455029X-RAY DIFFRACTION100
1.9402-2.02850.1322600.1065080X-RAY DIFFRACTION100
2.0285-2.13550.11832670.10795053X-RAY DIFFRACTION99
2.1355-2.26930.12832300.1155117X-RAY DIFFRACTION100
2.2693-2.44450.1362520.12045127X-RAY DIFFRACTION100
2.4445-2.69040.133050.12555058X-RAY DIFFRACTION100
2.6904-3.07960.15113060.13165078X-RAY DIFFRACTION99
3.0796-3.87950.15582720.12945168X-RAY DIFFRACTION100
3.8795-41.00770.152780.13855287X-RAY DIFFRACTION99

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