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- PDB-5ekw: A. thaliana IGPD2 in complex with the racemate of the triazole-ph... -

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Basic information

Entry
Database: PDB / ID: 5ekw
TitleA. thaliana IGPD2 in complex with the racemate of the triazole-phosphonate inhibitor, C348
ComponentsImidazoleglycerol-phosphate dehydratase 2, chloroplastic
KeywordsLYASE / Herbicide development / Histidine biosynthesis / Inhibitor complex / Dehydratase
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / chloroplast / metal ion binding
Similarity search - Function
Imidazole glycerol phosphate dehydratase; domain 1 / Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5DL / Chem-5LD / : / Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R.C. / Hawkes, T.R. / Baker, P.J. / Rice, D.W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide.
Authors: Bisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R.C. / Hawkes, T.R. / Baker, P.J. / Rice, D.W.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 2.0Nov 28, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id
Revision 2.1Oct 9, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 2.2Jan 10, 2024Group: 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
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_alt_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.pdbx_ptnr2_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,56714
Polymers22,3911
Non-polymers1,17613
Water4,089227
1
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)565,618336
Polymers537,38724
Non-polymers28,231312
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation22_555z,-y,x1
Buried area95030 Å2
ΔGint-301 kcal/mol
Surface area134210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.905, 112.905, 112.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-407-

EDO

21A-407-

EDO

31A-407-

EDO

41A-411-

TRS

51A-411-

TRS

61A-412-

TRS

71A-412-

TRS

81A-413-

CL

91A-723-

HOH

101A-725-

HOH

111A-727-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Imidazoleglycerol-phosphate dehydratase 2, chloroplastic / IGPD 2 / Protein HISTIDINE BIOSYNTHESIS 5B / Imidazoleglycerolphosphate-dehydratase isoform 2 / IGPD2


Mass: 22391.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Construct B represents the mature polypeptide (residues 69-272), excluding an N-terminal signal peptide. No electron density was visible for the residues before S75, which was renumbered S9 ...Details: Construct B represents the mature polypeptide (residues 69-272), excluding an N-terminal signal peptide. No electron density was visible for the residues before S75, which was renumbered S9 for consistency with the structure of A. thaliana IGPD1 (PDB: 2F1D).
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HISN5B, At4g14910, dl3495c / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase

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Non-polymers , 7 types, 240 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-5DL / [(2S)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid / (S)-C348


Mass: 207.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N3O4P
#4: Chemical ChemComp-5LD / [(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid / (R)-C348


Mass: 207.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N3O4P
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH8.5 and 20% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9507 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 1.1→35.7 Å / Num. all: 98895 / Num. obs: 98895 / % possible obs: 99.5 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.1
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QNK

4qnk


Resolution: 1.1→35.7 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.594 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13258 4953 5 %RANDOM
Rwork0.12348 ---
obs0.12394 93872 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.171 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.1→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 69 227 1790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191674
X-RAY DIFFRACTIONr_bond_other_d0.0040.021618
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9842268
X-RAY DIFFRACTIONr_angle_other_deg1.58633730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73123.46278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73115281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021876
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02386
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5751.126809
X-RAY DIFFRACTIONr_mcbond_other2.5771.119805
X-RAY DIFFRACTIONr_mcangle_it2.91.6911012
X-RAY DIFFRACTIONr_mcangle_other2.8991.6931013
X-RAY DIFFRACTIONr_scbond_it5.1441.436865
X-RAY DIFFRACTIONr_scbond_other5.141.434865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3341.9981246
X-RAY DIFFRACTIONr_long_range_B_refined5.54611.2522015
X-RAY DIFFRACTIONr_long_range_B_other5.5511.2622016
X-RAY DIFFRACTIONr_rigid_bond_restr9.62233290
X-RAY DIFFRACTIONr_sphericity_free25.219538
X-RAY DIFFRACTIONr_sphericity_bonded16.51453462
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 353 -
Rwork0.228 6745 -
obs--98.01 %

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