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- PDB-7oj5: Cryo-EM structure of Medicago truncatula HISN5 protein -

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Basic information

Entry
Database: PDB / ID: 7oj5
TitleCryo-EM structure of Medicago truncatula HISN5 protein
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / histidine biosynthesis / herbicide design / high-resolution Cryo-EM
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process
Similarity search - Function
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-type fold
Similarity search - Domain/homology
: / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRuszkowski, M. / Witek, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/D/NZ1/03630 Poland
CitationJournal: To Be Published
Title: Cryo-EM and crystal structures of a herbicide development target, HISN5
Authors: Witek, W. / Ruszkowski, M.
History
DepositionMay 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase
B: Imidazoleglycerol-phosphate dehydratase
C: Imidazoleglycerol-phosphate dehydratase
D: Imidazoleglycerol-phosphate dehydratase
E: Imidazoleglycerol-phosphate dehydratase
F: Imidazoleglycerol-phosphate dehydratase
G: Imidazoleglycerol-phosphate dehydratase
H: Imidazoleglycerol-phosphate dehydratase
I: Imidazoleglycerol-phosphate dehydratase
J: Imidazoleglycerol-phosphate dehydratase
K: Imidazoleglycerol-phosphate dehydratase
L: Imidazoleglycerol-phosphate dehydratase
M: Imidazoleglycerol-phosphate dehydratase
N: Imidazoleglycerol-phosphate dehydratase
O: Imidazoleglycerol-phosphate dehydratase
P: Imidazoleglycerol-phosphate dehydratase
Q: Imidazoleglycerol-phosphate dehydratase
R: Imidazoleglycerol-phosphate dehydratase
S: Imidazoleglycerol-phosphate dehydratase
T: Imidazoleglycerol-phosphate dehydratase
V: Imidazoleglycerol-phosphate dehydratase
W: Imidazoleglycerol-phosphate dehydratase
X: Imidazoleglycerol-phosphate dehydratase
Y: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,25672
Polymers544,61924
Non-polymers2,63748
Water16,772931
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "V"
d_22ens_1chain "W"
d_23ens_1chain "X"
d_24ens_1chain "Y"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAARGA1 - 184
d_12ens_1MNMNY
d_21ens_1ALAARGB1 - 184
d_22ens_1MNMNAA
d_31ens_1ALAARGC1 - 184
d_32ens_1MNMNCA
d_41ens_1ALAARGD1 - 184
d_42ens_1MNMNEA
d_51ens_1ALAARGE1 - 184
d_52ens_1MNMNGA
d_61ens_1ALAARGF1 - 184
d_62ens_1MNMNIA
d_71ens_1ALAARGG1 - 184
d_72ens_1MNMNKA
d_81ens_1ALAARGH1 - 184
d_82ens_1MNMNMA
d_91ens_1ALAARGI1 - 184
d_92ens_1MNMNOA
d_101ens_1ALAARGJ1 - 184
d_102ens_1MNMNQA
d_111ens_1ALAARGK1 - 184
d_112ens_1MNMNSA
d_121ens_1ALAARGL1 - 184
d_122ens_1MNMNUA
d_131ens_1ALAARGM1 - 184
d_132ens_1MNMNWA
d_141ens_1ALAARGN1 - 184
d_142ens_1MNMNYA
d_151ens_1ALAARGO1 - 184
d_152ens_1MNMNAB
d_161ens_1ALAARGP1 - 184
d_162ens_1MNMNCB
d_171ens_1ALAARGQ1 - 184
d_172ens_1MNMNEB
d_181ens_1ALAARGR1 - 184
d_182ens_1MNMNGB
d_191ens_1ALAARGS1 - 184
d_192ens_1MNMNIB
d_201ens_1ALAARGT1 - 184
d_202ens_1MNMNKB
d_211ens_1ALAARGU1 - 184
d_212ens_1MNMNMB
d_221ens_1ALAARGV1 - 184
d_222ens_1MNMNOB
d_231ens_1ALAARGW1 - 184
d_232ens_1MNMNQB
d_241ens_1ALAARGX1 - 184
d_242ens_1MNMNSB

NCS oper:
IDCodeMatrixVector
1given(1), (-1), (1)302.720001018
2given(-1), (-1), (1)302.719994019, 302.720002546
3given(-1), (1), (-1)302.719994506, 302.720012192
4given(-1), (1), (1)302.720000701
5given(-1), (-1), (-1)302.719994019, 302.72000251, 302.720002546
6given(1), (-1), (-1)302.720008705, 302.720001018
7given(-1), (1), (1)302.716601838
8given(1), (-1), (-1)302.719994019, 302.720002547
9given(1), (1), (-1)302.720012192
10given(1), (-1), (1)302.720012192
11given(1), (1), (1)
12given(-1), (-1), (-1)302.72000251, 302.720002546, 302.719994019
13given(-1), (-1), (1)302.720008705, 302.720001018
14given(1), (1), (1)
15given(-1), (1), (-1)302.720002546, 302.719994019
16given(-1), (1), (1)302.720001018
17given(1), (-1), (-1)302.720012192, 302.719994506
18given(1), (1), (-1)302.720000701
19given(-1), (1), (-1)302.720001018, 302.720008705
20given(-1), (-1), (-1)302.720002546, 302.719994019, 302.72000251
21given(1), (-1), (1)302.720000701
22given(1), (1), (-1)302.720001018
23given(-1), (-1), (1)302.720012192, 302.719994506

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Components

#1: Protein ...
Imidazoleglycerol-phosphate dehydratase


Mass: 22692.453 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I3SDM5, imidazoleglycerol-phosphate dehydratase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Medicago truncatula HISN5 protein / Type: COMPLEX / Details: Imidazoleglycerol-phosphate dehydratase / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Medicago truncatula (barrel medic)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1008

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
EM software
IDNameVersionCategoryDetails
1RELION3.1particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7PHENIX1.19-4092model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
13PHENIX1.19-4092model refinementreal-space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229366 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6EZJ

6ezj


Accession code: 6EZJ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 18.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001934992
ELECTRON MICROSCOPYf_angle_d0.51447352
ELECTRON MICROSCOPYf_chiral_restr0.04265400
ELECTRON MICROSCOPYf_plane_restr0.00326240
ELECTRON MICROSCOPYf_dihedral_angle_d4.31224728
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints1.65706486177E-13
ens_1d_3AELECTRON MICROSCOPYNCS constraints3.72958914564E-5
ens_1d_4AELECTRON MICROSCOPYNCS constraints5.27564445605E-5
ens_1d_5AELECTRON MICROSCOPYNCS constraints3.7282915355E-5
ens_1d_6AELECTRON MICROSCOPYNCS constraints5.27564445594E-5
ens_1d_7AELECTRON MICROSCOPYNCS constraints3.72829153542E-5
ens_1d_8AELECTRON MICROSCOPYNCS constraints0.000706586252387
ens_1d_9AELECTRON MICROSCOPYNCS constraints3.72958914545E-5
ens_1d_10AELECTRON MICROSCOPYNCS constraints3.72958914545E-5
ens_1d_11AELECTRON MICROSCOPYNCS constraints3.72958914548E-5
ens_1d_12AELECTRON MICROSCOPYNCS constraints0
ens_1d_13AELECTRON MICROSCOPYNCS constraints5.27564445611E-5
ens_1d_14AELECTRON MICROSCOPYNCS constraints3.72829153544E-5
ens_1d_15AELECTRON MICROSCOPYNCS constraints0
ens_1d_16AELECTRON MICROSCOPYNCS constraints3.72958914564E-5
ens_1d_17AELECTRON MICROSCOPYNCS constraints1.86103091251E-13
ens_1d_18AELECTRON MICROSCOPYNCS constraints5.27564445611E-5
ens_1d_19AELECTRON MICROSCOPYNCS constraints3.72829153553E-5
ens_1d_20AELECTRON MICROSCOPYNCS constraints3.72829153553E-5
ens_1d_21AELECTRON MICROSCOPYNCS constraints5.27564445602E-5
ens_1d_22AELECTRON MICROSCOPYNCS constraints3.72829153542E-5
ens_1d_23AELECTRON MICROSCOPYNCS constraints2.11936877614E-13
ens_1d_24AELECTRON MICROSCOPYNCS constraints5.27564445595E-5

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