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- PDB-4n7q: Crystal structure of eukaryotic THIC from A. thaliana -

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Basic information

Entry
Database: PDB / ID: 4n7q
TitleCrystal structure of eukaryotic THIC from A. thaliana
ComponentsPhosphomethylpyrimidine synthase, chloroplastic
KeywordsLYASE / (alpha/beta)8 TIM barrel fold / HMP-P synthase / SAM radical dependent enzyme / metal binding site
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
: / HEXANE-1,6-DIOL / Phosphomethylpyrimidine synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCoquille, S.C. / Roux, C. / Mehta, A. / Begley, T.P. / Fitzpatrick, T.B. / Thore, S.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: High-resolution crystal structure of the eukaryotic HMP-P synthase (THIC) from Arabidopsis thaliana.
Authors: Coquille, S. / Roux, C. / Mehta, A. / Begley, T.P. / Fitzpatrick, T.B. / Thore, S.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 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)65,9605
Polymers65,5461
Non-polymers4134
Water12,520695
1
A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules

A: Phosphomethylpyrimidine synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,91910
Polymers131,0922
Non-polymers8278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area7080 Å2
ΔGint-50 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.000, 107.000, 88.300
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-919-

HOH

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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: 65546.062 Da / Num. of mol.: 1 / Fragment: deltaN71-AtTHIC (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 / Production host: Escherichia coli (E. coli)
References: UniProt: O82392, phosphomethylpyrimidine synthase
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.01 M cobalt (II) chloride hexahydrate, 0.1 M sodium acetate trihydrate, 1 M 1,6-Hexanediol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 26, 2012
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 1.6→41.05 Å / Num. all: 77116 / Num. obs: 77101 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 13.58
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 9.95 % / Rmerge(I) obs: 1.271 / Mean I/σ(I) obs: 2.35 / Num. unique all: 5668 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EPM

3epm


Resolution: 1.6→41.027 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.176 6002 7.79 %RANDOM
Rwork0.1519 ---
obs0.1538 77088 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→41.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 25 695 4472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073945
X-RAY DIFFRACTIONf_angle_d1.0685355
X-RAY DIFFRACTIONf_dihedral_angle_d13.5471464
X-RAY DIFFRACTIONf_chiral_restr0.078570
X-RAY DIFFRACTIONf_plane_restr0.005701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.25781980.24362332X-RAY DIFFRACTION100
1.6182-1.63720.26472000.23372344X-RAY DIFFRACTION100
1.6372-1.65720.28251980.23182335X-RAY DIFFRACTION100
1.6572-1.67820.24111980.22432356X-RAY DIFFRACTION100
1.6782-1.70020.25522010.22082355X-RAY DIFFRACTION100
1.7002-1.72350.26061960.20852331X-RAY DIFFRACTION100
1.7235-1.74820.23732010.19872361X-RAY DIFFRACTION100
1.7482-1.77430.20831960.19882342X-RAY DIFFRACTION100
1.7743-1.8020.21682000.19332370X-RAY DIFFRACTION100
1.802-1.83150.24811960.19582330X-RAY DIFFRACTION100
1.8315-1.86310.21990.1882353X-RAY DIFFRACTION100
1.8631-1.8970.22091980.18192356X-RAY DIFFRACTION100
1.897-1.93350.20832000.18062354X-RAY DIFFRACTION100
1.9335-1.97290.22231990.16812361X-RAY DIFFRACTION100
1.9729-2.01580.1882000.16422373X-RAY DIFFRACTION100
2.0158-2.06270.17651970.16122366X-RAY DIFFRACTION100
2.0627-2.11430.17851990.15442338X-RAY DIFFRACTION100
2.1143-2.17150.15331970.15252355X-RAY DIFFRACTION100
2.1715-2.23540.18641990.15112376X-RAY DIFFRACTION100
2.2354-2.30750.19731990.15582372X-RAY DIFFRACTION100
2.3075-2.390.16461970.15072371X-RAY DIFFRACTION100
2.39-2.48570.18321960.14332384X-RAY DIFFRACTION100
2.4857-2.59880.15692010.13842370X-RAY DIFFRACTION100
2.5988-2.73570.1632010.13782364X-RAY DIFFRACTION100
2.7357-2.90710.17081980.14022400X-RAY DIFFRACTION100
2.9071-3.13150.16492010.1362387X-RAY DIFFRACTION100
3.1315-3.44650.16162040.1352398X-RAY DIFFRACTION100
3.4465-3.94480.1312090.1222404X-RAY DIFFRACTION100
3.9448-4.96870.12382040.10792430X-RAY DIFFRACTION100
4.9687-41.04090.14572200.1282518X-RAY DIFFRACTION100

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