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- PDB-4s29: Crystal structure of Arabidopsis thaliana ThiC with bound imidazo... -

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Basic information

Entry
Database: PDB / ID: 4s29
TitleCrystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide 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 diphosphate biosynthetic process / thiamine biosynthetic process / plastid / chloroplast stroma / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding ...phosphomethylpyrimidine synthase / response to vitamin B1 / carbon-carbon lyase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / plastid / chloroplast stroma / iron-sulfur cluster binding / chloroplast / 4 iron, 4 sulfur cluster binding / protein domain specific binding / metal ion binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #620 / Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #620 / Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / : / Chem-IRN / Phosphomethylpyrimidine synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.382 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.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)65,0964
Polymers64,6701
Non-polymers4263
Water9,692538
1
A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules

A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1928
Polymers129,3402
Non-polymers8526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5600 Å2
ΔGint-76 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.292, 107.292, 87.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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, At2g29630, T27A16.27 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O82392, phosphomethylpyrimidine synthase
#2: 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
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 43.41 %
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: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 118292 / Num. obs: 118249 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 10.25 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.38-1.435.10.317193.7
1.43-1.495.50.239198.3
1.49-1.555.30.173199
1.55-1.645.20.129199
1.64-1.745.60.105199.4
1.74-1.875.20.081199.4
1.87-2.065.60.063199.8
2.06-2.365.40.051199.8
2.36-2.975.60.0451100
2.97-505.30.038199.8

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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: 1.382→46.459 Å / SU ML: 0.1 / σ(F): 1.39 / Phase error: 11.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1433 5812 4.92 %
Rwork0.1187 --
obs0.1199 118249 99.13 %
all-118292 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.0215 Å2
Refinement stepCycle: LAST / Resolution: 1.382→46.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 25 538 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054126
X-RAY DIFFRACTIONf_angle_d1.0545638
X-RAY DIFFRACTIONf_dihedral_angle_d12.4961528
X-RAY DIFFRACTIONf_chiral_restr0.071602
X-RAY DIFFRACTIONf_plane_restr0.005742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3816-1.39730.21081960.15633578X-RAY DIFFRACTION95
1.3973-1.41370.17191790.14093635X-RAY DIFFRACTION97
1.4137-1.43090.17981740.12413698X-RAY DIFFRACTION98
1.4309-1.44910.15181670.11773678X-RAY DIFFRACTION98
1.4491-1.46810.15722170.11343658X-RAY DIFFRACTION98
1.4681-1.48820.14011840.10983701X-RAY DIFFRACTION99
1.4882-1.50950.15621990.1063714X-RAY DIFFRACTION99
1.5095-1.5320.14532120.10213698X-RAY DIFFRACTION99
1.532-1.5560.13421690.10163751X-RAY DIFFRACTION99
1.556-1.58150.13721810.13699X-RAY DIFFRACTION99
1.5815-1.60880.13651550.10313755X-RAY DIFFRACTION99
1.6088-1.6380.13021780.09963715X-RAY DIFFRACTION99
1.638-1.66950.13372050.09873783X-RAY DIFFRACTION99
1.6695-1.70360.12771620.10073723X-RAY DIFFRACTION99
1.7036-1.74060.13092140.10213719X-RAY DIFFRACTION99
1.7406-1.78110.14351880.10423760X-RAY DIFFRACTION99
1.7811-1.82570.14542070.10513768X-RAY DIFFRACTION99
1.8257-1.8750.13331710.11143754X-RAY DIFFRACTION99
1.875-1.93020.13652170.11163727X-RAY DIFFRACTION100
1.9302-1.99250.14492070.11053747X-RAY DIFFRACTION100
1.9925-2.06370.13242090.11263776X-RAY DIFFRACTION100
2.0637-2.14640.13941890.11333785X-RAY DIFFRACTION100
2.1464-2.24410.13991650.11343785X-RAY DIFFRACTION100
2.2441-2.36240.13591830.11553813X-RAY DIFFRACTION100
2.3624-2.51040.13442110.11833803X-RAY DIFFRACTION100
2.5104-2.70420.12942180.12193766X-RAY DIFFRACTION100
2.7042-2.97630.13912100.12843805X-RAY DIFFRACTION100
2.9763-3.40680.1442060.13363808X-RAY DIFFRACTION100
3.4068-4.29180.16372340.12653855X-RAY DIFFRACTION100
4.2918-46.48510.1432050.13733980X-RAY DIFFRACTION100

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