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- PDB-5el9: A. thaliana IGPD2 in complex with the triazole-phosphonate inhibi... -

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Basic information

Entry
Database: PDB / ID: 5el9
TitleA. thaliana IGPD2 in complex with the triazole-phosphonate inhibitor, (S)-C348, to 1.1A resolution
ComponentsImidazoleglycerol-phosphate dehydratase 2, chloroplastic
KeywordsLYASE / Herbicide discovery / Histidine biosynthesis / Inhibitor complex / Dehydratase
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / 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 / : / 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.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
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 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,26512
Polymers22,3911
Non-polymers87411
Water3,675204
1
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,354288
Polymers537,38724
Non-polymers20,967264
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Unit cell
Length a, b, c (Å)112.620, 112.620, 112.620
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-304-

TRS

21A-304-

TRS

31A-406-

HOH

41A-458-

HOH

51A-475-

HOH

61A-575-

HOH

71A-580-

HOH

81A-601-

HOH

91A-603-

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 / Fragment: UNP residues 69-272
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 , 5 types, 215 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5 and 15% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.1→45.98 Å / Num. all: 98751 / Num. obs: 98751 / % possible obs: 99.6 % / Redundancy: 16.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 28
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.9 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
REFMACdirect refinementphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EKW

5ekw


Resolution: 1.1→45.98 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.522 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12917 4815 4.9 %RANDOM
Rwork0.11377 ---
obs0.11453 93396 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.997 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 51 204 1788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191687
X-RAY DIFFRACTIONr_bond_other_d0.0030.021662
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9712281
X-RAY DIFFRACTIONr_angle_other_deg1.59833821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15122.69278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1611517
X-RAY DIFFRACTIONr_chiral_restr0.1150.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021901
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02400
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_it2.8230.867821
X-RAY DIFFRACTIONr_mcbond_other2.8110.864819
X-RAY DIFFRACTIONr_mcangle_it3.6281.3131030
X-RAY DIFFRACTIONr_mcangle_other3.6291.3151031
X-RAY DIFFRACTIONr_scbond_it10.6341.297866
X-RAY DIFFRACTIONr_scbond_other10.6321.297866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.0131.7291242
X-RAY DIFFRACTIONr_long_range_B_refined8.6348.781951
X-RAY DIFFRACTIONr_long_range_B_other8.6328.7861952
X-RAY DIFFRACTIONr_rigid_bond_restr13.76833348
X-RAY DIFFRACTIONr_sphericity_free48.218555
X-RAY DIFFRACTIONr_sphericity_bonded21.3553472
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 334 -
Rwork0.188 6601 -
obs--96.72 %

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