PDB-8ci0: Maize Transketolase in complex with TPP and hydrolyzed (+)-Cornexistin

ID or keywords:

Entry

Database: PDB / ID: 8ci0

Title

Maize Transketolase in complex with TPP and hydrolyzed (+)-Cornexistin

Components

Transketolase, chloroplastic

Keywords

TRANSFERASE /

Herbicide

Function / homology

Function and homology information

transketolase /

transketolase activity / reductive pentose-phosphate cycle / pentose-phosphate shunt / cobalt ion binding / chloroplast thylakoid membrane / manganese ion binding /

calcium ion binding /

cytosol
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.902 Å

Authors

Freigang, J.

Funding support

1items

Citation

Journal: Chemistry / Year: 2023
Title: Investigations into Simplified Analogues of the Herbicidal Natural Product (+)-Cornexistin.
Authors: Steinborn, C. / Tancredi, A. / Habiger, C. / Diederich, C. / Kramer, J. / Reingruber, A.M. / Laber, B. / Freigang, J. / Lange, G. / Schmutzler, D. / Machettira, A. / Besong, G. / Magauer, T. / Barber, D.M.

History

Deposition	Feb 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 26, 2023	Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim Item: _citation.journal_volume / _citation_author.identifier_ORCID ..._citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ci0.cif.gz	444.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8ci0.ent.gz		Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/8ci0 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/8ci0	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (8) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (4)

Deposited unit

AAA: Transketolase, chloroplastic

BBB: Transketolase, chloroplastic

CCC: Transketolase, chloroplastic

hetero molecules

226 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	135.309, 135.309, 201.439
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	CCC-1167- HOH
2	1	CCC-1392- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	BBB
6	3	CCC

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 10 - 675 / Label seq-ID: 23 - 688

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	2	1	BBB	B
3	3	2	AAA	A
4	4	2	CCC	C
5	5	3	BBB	B
6	6	3	CCC	C

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Protein , 1 types, 3 molecules AAABBBCCC

#1: Protein	Transketolase, chloroplastic / / TK Mass: 74830.156 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIC9, transketolase

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Non-polymers , 5 types, 2021 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-UP0 / (1~{Z},3~{R},4~{S},7~{S},8~{Z})-8-ethylidene-4,7-bis(oxidanyl)-5-oxidanylidene-3-propyl-cyclononene-1,2-dicarboxylic acid Mass: 326.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₂₂O₇ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-8EL / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate Mass: 426.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₀N₄O₇P₂S
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2014 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.13 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 28 % PEG 3350, 250 mM ammonium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
Detector	Type: OXFORD ONYX CCD / Detector: CCD / Date: Oct 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.9→23.83 Å / Num. obs: 157602 / % possible obs: 94.4 % / Redundancy: 6.01 % / R_merge(I) obs: 0.064 / Net I/σ(I): 19
Reflection shell	Resolution: 1.9→2 Å / R_merge(I) obs: 0.175 / Num. unique obs: 18870

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
CrysalisPro		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.902→23.727 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.933 / SU B: 2.494 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1836	7754	4.921 %
R_work	0.1532	149805	-
all	0.155	-	-
obs	-	157559	94.208 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 11.924 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.127 Å²	0.064 Å²	0 Å²
2-	-	0.127 Å²	-0 Å²
3-	-	-	-0.414 Å²

Refinement step

Cycle: LAST / Resolution: 1.902→23.727 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15246	0	104	2014	17364

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	15611
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14432
X-RAY DIFFRACTION	r_angle_refined_deg	1.544	1.641	21215
X-RAY DIFFRACTION	r_angle_other_deg	1.488	1.578	33253
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.691	5	1995
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.725	22.591	745
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.957	15	2434
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.559	15	75
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	2041
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	17956
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3488
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	3586
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	14362
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	7786
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	6917
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	1425
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.027	0.2	5
X-RAY DIFFRACTION	r_metal_ion_refined	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.255	0.2	39
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	152
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.245	0.2	74
X-RAY DIFFRACTION	r_mcbond_it	0.919	1.105	7989
X-RAY DIFFRACTION	r_mcbond_other	0.915	1.104	7988
X-RAY DIFFRACTION	r_mcangle_it	1.346	1.651	9981
X-RAY DIFFRACTION	r_mcangle_other	1.347	1.651	9982
X-RAY DIFFRACTION	r_scbond_it	1.71	1.266	7622
X-RAY DIFFRACTION	r_scbond_other	1.711	1.266	7615
X-RAY DIFFRACTION	r_scangle_it	2.638	1.835	11234
X-RAY DIFFRACTION	r_scangle_other	2.638	1.835	11235
X-RAY DIFFRACTION	r_lrange_it	4.267	14.492	18703
X-RAY DIFFRACTION	r_lrange_other	3.903	13.93	18201
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.052	0.05	22111
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.049	0.05	22224
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.043	0.05	22239

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.05243	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.05243	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.04912	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.04912	0.05009
3	5	BBB	X-RAY DIFFRACTION	Local ncs	0.04347	0.05009
3	6	CCC	X-RAY DIFFRACTION	Local ncs	0.04347	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.902-1.951	0.249	472	0.192	8307	X-RAY DIFFRACTION	71.6185
1.951-2.004	0.221	447	0.179	9635	X-RAY DIFFRACTION	84.3823
2.004-2.063	0.195	483	0.163	9724	X-RAY DIFFRACTION	87.9459
2.063-2.126	0.199	486	0.153	9722	X-RAY DIFFRACTION	90.2325
2.126-2.196	0.191	516	0.144	9619	X-RAY DIFFRACTION	92.5994
2.196-2.273	0.176	479	0.137	9610	X-RAY DIFFRACTION	95.1075
2.273-2.358	0.159	554	0.131	9426	X-RAY DIFFRACTION	97.2804
2.358-2.455	0.179	481	0.132	9313	X-RAY DIFFRACTION	99.1195
2.455-2.564	0.188	423	0.134	9039	X-RAY DIFFRACTION	99.9683
2.564-2.689	0.17	442	0.136	8619	X-RAY DIFFRACTION	100
2.689-2.834	0.179	394	0.144	8265	X-RAY DIFFRACTION	99.9885
2.834-3.006	0.2	389	0.158	7780	X-RAY DIFFRACTION	99.9755
3.006-3.214	0.19	400	0.159	7299	X-RAY DIFFRACTION	100
3.214-3.471	0.188	403	0.171	6791	X-RAY DIFFRACTION	99.9861
3.471-3.802	0.186	329	0.169	6283	X-RAY DIFFRACTION	99.9849
3.802-4.25	0.156	313	0.146	5710	X-RAY DIFFRACTION	99.9502
4.25-4.906	0.17	259	0.146	5074	X-RAY DIFFRACTION	99.9063
4.906-6.006	0.178	218	0.175	4319	X-RAY DIFFRACTION	99.9559
6.006-8.483	0.178	161	0.162	3416	X-RAY DIFFRACTION	99.9721
8.483-23.727	0.174	105	0.181	1855	X-RAY DIFFRACTION	94.0951

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Protein , 1 types, 3 molecules AAABBBCCC

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