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- PDB-8zx0: Crystal Structure of CntL in complex with a dual-site inhibitor -

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Open data

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Basic information

Entry

Database: PDB / ID: 8zx0

Title

Crystal Structure of CntL in complex with a dual-site inhibitor

Components

D-histidine 2-aminobutanoyltransferase

Keywords

TRANSFERASE / inhibitor

Function / homology

D-histidine 2-aminobutanoyltransferase / nicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / CYSTEINE / D-histidine 2-aminobutanoyltransferase

Function and homology information

Biological species

Staphylococcus aureus subsp. aureus Mu50 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.091 Å

Authors

Luo, Z. / Zhou, H.

Funding support

China, 2items

Citation

Journal: Eur.J.Med.Chem. / Year: 2024
Title: Structure-guided inhibitor design targeting CntL provides the first chemical validation of the staphylopine metallophore system in bacterial metal acquisition.
Authors: Luo, Z. / Su, J. / Luo, S. / Ju, Y. / Chen, B. / Gu, Q. / Zhou, H.

History

Deposition	Jun 13, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	8zx0.cif.gz	262.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8zx0.ent.gz		Display	PDB format
PDBx/mmJSON format	8zx0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/8zx0 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/8zx0	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	#111 - Mar 2009 Hydrogenase similarity (1) #149 - May 2012 Leptin similarity (1)

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Assembly

Deposited unit

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

65.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
262 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.395, 135.511, 131.814
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein

D-histidine 2-aminobutanoyltransferase / Nicotianamine synthase-like enzyme / NAS

Mass: 31958.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: cntL, SAV2469 / Production host:

Escherichia coli (E. coli)
References: UniProt: A0A0H3JXA8, D-histidine 2-aminobutanoyltransferase

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Non-polymers , 5 types, 118 molecules

#2: Chemical	ChemComp-A1D9C / (2S)-2-[2-[[(2S,3S,4R,5R)-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethylamino]-3-(1H-imidazol-4-yl)propanoic acid Mass: 498.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₂₃ClN₈O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CYS / CYSTEINE Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₂S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.56 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.23 M Calcium acetate, 0.1 M Sodium cacodylate 6.4, 35% PEG 300, 1.5% iBu

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 2.09→67.76 Å / Num. obs: 29426 / % possible obs: 97.1 % / Redundancy: 5.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.09→2.2 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.853 / Num. unique obs: 4341 / CC_1/2: 0.668 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
autoPROC		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.091→67.756 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.255 / WR_factor R_work: 0.213 / SU B: 11.576 / SU ML: 0.149 / Average fsc free: 0.9605 / Average fsc work: 0.9743 / Cross valid method: FREE R-VALUE / ESU R: 0.244 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2393	1475	5.02 %
R_work	0.2014	27909	-
all	0.203	-	-
obs	-	29384	96.974 %

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: 41.628 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.585 Å²	0 Å²	-0 Å²
2-	-	-2.244 Å²	0 Å²
3-	-	-	-1.342 Å²

Refinement step

Cycle: LAST / Resolution: 2.091→67.756 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3701	0	97	109	3907

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	3856
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3640
X-RAY DIFFRACTION	r_angle_refined_deg	1.175	1.645	5237
X-RAY DIFFRACTION	r_angle_other_deg	0.418	1.588	8323
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.623	5	480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.154	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.447	10	583
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.2	10	154
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	630
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4485
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	827
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	723
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	3178
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1907
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	2101
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	118
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.013	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.232	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.131	0.2	19
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.09	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.85	2.501	1941
X-RAY DIFFRACTION	r_mcbond_other	1.85	2.501	1941
X-RAY DIFFRACTION	r_mcangle_it	2.906	4.467	2414
X-RAY DIFFRACTION	r_mcangle_other	2.908	4.47	2415
X-RAY DIFFRACTION	r_scbond_it	2.775	2.815	1915
X-RAY DIFFRACTION	r_scbond_other	2.774	2.817	1916
X-RAY DIFFRACTION	r_scangle_it	4.382	5.042	2823
X-RAY DIFFRACTION	r_scangle_other	4.381	5.045	2824
X-RAY DIFFRACTION	r_lrange_it	6.859	27.029	4111
X-RAY DIFFRACTION	r_lrange_other	6.846	27.01	4106

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
2.091-2.145	0.272	99	0.25	2082	0.251	2185	0.955	0.967	99.8169	0.228
2.145-2.204	0.307	103	0.246	2047	0.249	2151	0.926	0.965	99.9535	0.225
2.204-2.268	0.263	72	0.246	1623	0.247	2100	0.943	0.966	80.7143	0.219
2.268-2.338	0.25	104	0.225	1935	0.226	2042	0.961	0.971	99.8531	0.196
2.338-2.414	0.236	105	0.216	1856	0.217	1961	0.959	0.973	100	0.188
2.414-2.499	0.225	115	0.215	1791	0.215	1907	0.969	0.972	99.9476	0.188
2.499-2.593	0.248	104	0.203	1763	0.205	1868	0.963	0.978	99.9465	0.174
2.593-2.699	0.274	83	0.206	1489	0.209	1795	0.959	0.977	87.5766	0.173
2.699-2.819	0.278	79	0.193	1628	0.196	1712	0.952	0.98	99.7079	0.174
2.819-2.956	0.248	71	0.195	1558	0.197	1630	0.964	0.979	99.9387	0.181
2.956-3.115	0.191	66	0.192	1489	0.192	1557	0.979	0.977	99.8715	0.186
3.115-3.304	0.256	68	0.188	1424	0.192	1493	0.965	0.979	99.933	0.188
3.304-3.532	0.185	51	0.182	1153	0.182	1393	0.976	0.98	86.4322	0.189
3.532-3.814	0.204	66	0.177	1226	0.178	1296	0.977	0.981	99.6914	0.189
3.814-4.176	0.247	68	0.171	1100	0.175	1209	0.962	0.984	96.6088	0.19
4.176-4.667	0.179	62	0.164	1034	0.165	1111	0.981	0.984	98.6499	0.196
4.667-5.385	0.246	55	0.189	919	0.192	976	0.965	0.979	99.7951	0.227
5.385-6.585	0.215	47	0.26	787	0.257	836	0.975	0.963	99.7608	0.309
6.585-9.268	0.264	40	0.228	629	0.23	669	0.968	0.971	100	0.307
9.268-67.756	0.45	17	0.264	376	0.272	404	0.887	0.96	97.2772	0.486

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.8223	0.2954	-3.4936	0.0206	-0.2211	2.5552	-0.4484	0.1645	-0.5521	-0.0344	-0.0017	-0.0558	0.3485	-0.047	0.4501	0.0647	0.0548	0.1001	0.4189	-0.0297	0.2948	31.344	9.2618	5.7195
2	2.8468	-0.1999	-1.6225	0.2425	-0.4999	2.5851	-0.1612	0.6839	-0.471	0.0764	-0.1877	-0.004	-0.0667	-0.002	0.3488	0.0478	-0.0823	-0.0052	0.4124	-0.1283	0.1552	22.6511	10.0111	10.0115
3	1.0025	0.6139	0.32	2.7534	0.5797	0.1655	-0.0885	0.011	-0.0629	0.1988	0.1837	-0.4328	0.0159	0.0183	-0.0952	0.1255	-0.0041	-0.0597	0.3066	-0.0465	0.209	18.1257	22.3689	28.9084
4	0.2948	-0.5912	0.3339	2.1552	-0.1238	0.8721	-0.0433	0.0574	-0.0501	0.3294	0.0659	0.1317	0.0591	-0.0466	-0.0226	0.0787	0.0161	0.0168	0.3542	-0.0224	0.2016	11.1531	15.8039	24.3829
5	1.6287	-0.8534	-0.4484	1.1573	0.6049	0.9432	0.0827	0.2868	0.0684	0.0549	-0.1036	-0.0604	-0.081	-0.0761	0.0209	0.0372	0.0187	-0.0006	0.3479	0.0049	0.2371	17.0649	27.9075	13.8517
6	0.6063	-0.1945	-0.8196	0.6081	0.2953	2.1814	-0.0659	-0.081	0.1753	-0.0522	0.0059	0.0039	0.3168	-0.0553	0.06	0.0681	-0.0205	0.0272	0.3621	0.0109	0.2182	-2.3929	11.8775	-3.3736
7	0.5585	1.1132	-0.0386	2.4667	-0.4069	0.7877	0.0163	0.1303	0.0859	0.0278	0.156	0.1395	0.0935	-0.0098	-0.1723	0.0471	-0.0234	-0.0111	0.3234	0.0563	0.2108	6.0538	15.7284	-26.5305
8	0.9357	1.1946	-0.3718	3.0305	-0.4807	1.1091	-0.1234	0.0141	-0.0128	-0.2517	0.146	-0.1352	0.098	0.2271	-0.0226	0.0516	0.0307	0.0159	0.2856	0.0113	0.1776	15.028	15.9058	-27.564
9	0.8381	0.3996	-0.5898	0.5351	-0.2649	0.5048	0.0341	-0.1136	0.0637	-0.0453	0.0345	0.0409	-0.0041	0.1006	-0.0686	0.0179	-0.0197	0.0015	0.3729	-0.0025	0.2441	10.3219	27.6141	-13.0169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	6 - 59
2	X-RAY DIFFRACTION	2	ALL	A	60 - 111
3	X-RAY DIFFRACTION	3	ALL	A	112 - 146
4	X-RAY DIFFRACTION	4	ALL	A	147 - 204
5	X-RAY DIFFRACTION	5	ALL	A	205 - 263
6	X-RAY DIFFRACTION	6		B	5 - 82
7	X-RAY DIFFRACTION	7		B	83 - 141
8	X-RAY DIFFRACTION	8		B	142 - 193
9	X-RAY DIFFRACTION	9		B	194 - 263

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