PDB-8b9m: Cysteine Synthase from Leishmania Infantum

ID or keywords:

Entry

Database: PDB / ID: 8b9m

Title

Cysteine Synthase from Leishmania Infantum

Components

Cysteine synthase

Keywords

UNKNOWN FUNCTION / Cysteine synthase / Amino acid synthesis / Leishmaniasis

Function / homology

Function and homology information

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

Biological species

Leishmania infantum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 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 6, 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 / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8b9m.cif.gz	249.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8b9m.ent.gz	196.2 KB	Display	PDB format
PDBx/mmJSON format	8b9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8b9m_validation.pdf.gz	453.1 KB	Display	wwPDB validaton report
Full document	8b9m_full_validation.pdf.gz	458.7 KB	Display
Data in XML	8b9m_validation.xml.gz	27.8 KB	Display
Data in CIF	8b9m_validation.cif.gz	40.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/8b9m ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b9m	HTTPS FTP

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Related structure data

Related structure data	8b9wC 8b9yC 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

B: Cysteine synthase

hetero molecules

75.1 kDa, 2 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)	48.879, 87.759, 138.073
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cysteine synthase Mass: 37427.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ_36_3750 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ID39, cysteine synthase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.82 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium Chloride, Bis-Tris, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.75→87.77 Å / Num. obs: 60590 / % possible obs: 99.6 % / Redundancy: 11.8 % / CC_1/2: 0.991 / Net I/σ(I): 11.96
Reflection shell	Resolution: 1.75→1.78 Å / Num. unique obs: 2908 / CC_1/2: 0.805

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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: 1.75→74.175 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.953 / SU B: 2.847 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2052	3030	5.007 %
R_work	0.1641	57490	-
all	0.166	-	-
obs	-	60520	99.554 %

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: 23.883 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.126 Å²	-0 Å²	-0 Å²
2-	-	-0.665 Å²	0 Å²
3-	-	-	0.791 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→74.175 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4516	0	15	404	4935

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4747
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4558
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.632	6471
X-RAY DIFFRACTION	r_angle_other_deg	0.507	1.551	10645
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.982	5	662
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.974	10	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.783	10	840
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.679	10	176
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	782
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5419
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	845
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	920
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	4269
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	2409
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2649
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	341
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.256	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	27
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.02	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.432	2.447	2492
X-RAY DIFFRACTION	r_mcbond_other	2.426	2.447	2492
X-RAY DIFFRACTION	r_mcangle_it	3.801	3.646	3122
X-RAY DIFFRACTION	r_mcangle_other	3.8	3.647	3123
X-RAY DIFFRACTION	r_scbond_it	3.227	2.765	2255
X-RAY DIFFRACTION	r_scbond_other	3.227	2.765	2256
X-RAY DIFFRACTION	r_scangle_it	4.967	3.999	3321
X-RAY DIFFRACTION	r_scangle_other	4.966	4	3322
X-RAY DIFFRACTION	r_lrange_it	7.111	36.245	5367
X-RAY DIFFRACTION	r_lrange_other	7.067	34.239	5266

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.75-1.795	0.29	233	0.286	4180	0.287	4427	0.935	0.935	99.6838	0.273
1.795-1.845	0.247	210	0.252	4036	0.252	4301	0.953	0.95	98.7212	0.234
1.845-1.898	0.247	211	0.219	3964	0.221	4227	0.957	0.963	98.7698	0.194
1.898-1.956	0.252	178	0.199	3872	0.201	4089	0.952	0.971	99.0462	0.173
1.956-2.021	0.219	219	0.182	3742	0.184	3962	0.969	0.977	99.9748	0.154
2.021-2.091	0.213	166	0.174	3647	0.176	3846	0.968	0.979	99.142	0.147
2.091-2.17	0.218	199	0.167	3459	0.17	3680	0.97	0.982	99.4022	0.142
2.17-2.259	0.202	184	0.156	3382	0.159	3584	0.977	0.984	99.4978	0.133
2.259-2.359	0.199	161	0.148	3270	0.15	3445	0.976	0.986	99.5936	0.123
2.359-2.474	0.183	163	0.143	3122	0.145	3295	0.978	0.987	99.6965	0.12
2.474-2.608	0.214	166	0.153	2951	0.156	3123	0.972	0.985	99.8079	0.129
2.608-2.766	0.207	154	0.16	2828	0.163	2986	0.972	0.984	99.866	0.137
2.766-2.957	0.207	134	0.162	2659	0.164	2795	0.972	0.983	99.9284	0.14
2.957-3.193	0.212	140	0.154	2487	0.157	2628	0.972	0.984	99.9619	0.139
3.193-3.497	0.204	116	0.169	2316	0.17	2432	0.972	0.983	100	0.155
3.497-3.909	0.206	91	0.153	2097	0.155	2188	0.973	0.986	100	0.143
3.909-4.511	0.161	96	0.13	1875	0.132	1971	0.985	0.99	100	0.128
4.511-5.52	0.176	89	0.143	1598	0.144	1687	0.988	0.99	100	0.142
5.52-7.785	0.212	72	0.175	1254	0.177	1326	0.978	0.984	100	0.172
7.785-74.175	0.188	48	0.155	751	0.157	799	0.979	0.983	100	0.173

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