PDB-8b9y: Cysteine Synthase from Trypanosoma cruzi with PLP and OAS

ID or keywords:

Entry

Database: PDB / ID: 8b9y

Title

Cysteine Synthase from Trypanosoma cruzi with PLP and OAS

Components

Cysteine synthase, putative

Keywords

TRANSFERASE /

Chagas disease /

amino acid synthesis / o-acetyl L-serine /

pyridoxal 5-phosphate

Function / homology

Function and homology information

cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sowerby, K.V. / Pohl, E.

Funding support

United Kingdom, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis.
Authors: Sowerby, K. / Freitag-Pohl, S. / Murillo, A.M. / Silber, A.M. / Pohl, E.

History

Deposition	Oct 10, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/8b9y ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b9y	HTTPS FTP

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Related structure data

Related structure data	8b9mC 8b9wC 4airS S: Starting model for refinement C: citing same article (ref.)
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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Cysteine synthase, putative

B: Cysteine synthase, putative

C: Cysteine synthase, putative

D: Cysteine synthase, putative

hetero molecules

148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cysteine synthase, putative

B: Cysteine synthase, putative

hetero molecules

defined by author&software
Evidence: gel filtration
74.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cysteine synthase, putative

D: Cysteine synthase, putative

hetero molecules

defined by author&software
Evidence: gel filtration
74 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.006, 66.667, 167.518
Angle α, β, γ (deg.)	90.000, 90.468, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	PHE	PHE	GLU	GLU	18 - 332	18 - 332
2	1	1	PHE	PHE	ILE	ILE	18 - 344	18 - 344
3	2	2	GLU	GLU	ILE	ILE	17 - 344	17 - 344
4	2	2	GLU	GLU	ILE	ILE	17 - 344	17 - 344
5	3	3	GLU	GLU	ILE	ILE	17 - 344	17 - 344
6	3	3	GLU	GLU	ILE	ILE	17 - 344	17 - 344
7	4	4	PHE	PHE	ASP	ASP	18 - 343	18 - 343
8	4	4	PHE	PHE	ASP	ASP	18 - 331	18 - 331
9	5	5	PHE	PHE	ILE	ILE	18 - 344	18 - 344
10	5	5	PHE	PHE	ILE	ILE	18 - 344	18 - 344
11	6	6	GLU	GLU	ILE	ILE	17 - 344	17 - 344
12	6	6	GLU	GLU	ILE	ILE	17 - 344	17 - 344

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
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein

Cysteine synthase, putative /

Mass: 36649.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053507165.50 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q4CST7

#3: Sugar

ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose /

Ribose

Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₀O₅

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Non-polymers , 4 types, 555 molecules

#2: Chemical	ChemComp-OAS / O-ACETYLSERINE / O-Acetylserine Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.26 Å³/Da / Density % sol: 45.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, Bis-Tis

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.8→54.94 Å / Num. obs: 110107 / % possible obs: 98.27 % / Redundancy: 3.37 % / CC_1/2: 0.9961 / Net I/σ(I): 12.93
Reflection shell	Resolution: 1.8→1.83 Å / Num. unique obs: 5376 / CC_1/2: 0.9059

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4AIR

4air

Resolution: 1.8→54.94 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.932 / SU B: 2.931 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2173	5483	4.98 %
R_work	0.1913	104624	-
all	0.193	-	-
obs	-	110107	97.867 %

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: 24.233 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.554 Å²	-0 Å²	-0.123 Å²
2-	-	0.046 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→54.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9335	0	92	548	9975

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	9661
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8985
X-RAY DIFFRACTION	r_angle_refined_deg	1.362	1.637	13177
X-RAY DIFFRACTION	r_angle_other_deg	0.468	1.546	20851
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.782	5	1301
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.185	10	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.507	10	1494
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.063	10	346
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1564
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11094
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1790
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	2044
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	8491
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	5002
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	5207
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	454
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.261	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	150
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.264	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	2.273	2.504	5147
X-RAY DIFFRACTION	r_mcbond_other	2.271	2.504	5147
X-RAY DIFFRACTION	r_mcangle_it	3.141	3.743	6431
X-RAY DIFFRACTION	r_mcangle_other	3.141	3.744	6432
X-RAY DIFFRACTION	r_scbond_it	2.942	2.785	4514
X-RAY DIFFRACTION	r_scbond_other	2.942	2.785	4515
X-RAY DIFFRACTION	r_scangle_it	4.293	4.059	6734
X-RAY DIFFRACTION	r_scangle_other	4.293	4.059	6735
X-RAY DIFFRACTION	r_lrange_it	6.025	36.564	10807
X-RAY DIFFRACTION	r_lrange_other	6.025	36.565	10808
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.103	0.05	8774
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	9354
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.101	0.05	8883
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.1	0.05	9357
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.076	0.05	9777
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.103	0.05	9438

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10327	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10327	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0645	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.0645	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10119	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10119	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.10014	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.10014	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07587	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07587	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10335	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10335	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 (%)
1.8-1.847	0.255	419	0.224	7504	X-RAY DIFFRACTION	96.3049
1.847-1.897	0.244	363	0.219	7431	X-RAY DIFFRACTION	96.4962
1.897-1.952	0.236	369	0.209	7272	X-RAY DIFFRACTION	97.6361
1.952-2.012	0.246	397	0.199	7017	X-RAY DIFFRACTION	97.3988
2.012-2.078	0.221	393	0.195	6781	X-RAY DIFFRACTION	97.4596
2.078-2.151	0.242	345	0.19	6654	X-RAY DIFFRACTION	97.5606
2.151-2.232	0.214	312	0.174	6434	X-RAY DIFFRACTION	97.7256
2.232-2.323	0.199	324	0.167	6168	X-RAY DIFFRACTION	97.8448
2.323-2.426	0.2	359	0.17	5863	X-RAY DIFFRACTION	97.9534
2.426-2.544	0.202	295	0.174	5721	X-RAY DIFFRACTION	97.9805
2.544-2.682	0.214	295	0.173	5380	X-RAY DIFFRACTION	97.9293
2.682-2.844	0.204	263	0.182	5142	X-RAY DIFFRACTION	98.7034
2.844-3.04	0.207	230	0.19	4916	X-RAY DIFFRACTION	98.6391
3.04-3.282	0.221	234	0.195	4525	X-RAY DIFFRACTION	98.7959
3.282-3.594	0.217	221	0.194	4185	X-RAY DIFFRACTION	99.1003
3.594-4.017	0.202	205	0.199	3791	X-RAY DIFFRACTION	98.9354
4.017-4.634	0.225	165	0.194	3376	X-RAY DIFFRACTION	98.9936
4.634-5.666	0.234	148	0.2	2857	X-RAY DIFFRACTION	99.2404
5.666-7.972	0.239	82	0.217	2284	X-RAY DIFFRACTION	98.9544
7.972-54.94	0.179	63	0.18	1292	X-RAY DIFFRACTION	98.2596

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