PDB-8e7q: Crystal Structure of FosB from Bacillus cereus with Zinc and 2-Ph...

ID or keywords:

Entry

Database: PDB / ID: 8e7q

Title

Crystal Structure of FosB from Bacillus cereus with Zinc and 2-Phosphonopropionic acid

Components

Metallothiol transferase FosB

Keywords

TRANSFERASE / inhibitor / 2-phosphonopropionic acid

Function / homology

Function and homology information

transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / response to antibiotic / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Travis, S. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.

Funding support

United States, 1items

Citation

Journal: Rsc Med Chem / Year: 2023
Title: Identification and analysis of small molecule inhibitors of FosB from Staphylococcus aureus.
Authors: Travis, S. / Green, K.D. / Thamban Chandrika, N. / Pang, A.H. / Frantom, P.A. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.

History

Deposition	Aug 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	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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PDBx/mmCIF format	8e7q.cif.gz	80.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8e7q_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8e7q_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8e7q_validation.xml.gz	15.4 KB	Display
Data in CIF	8e7q_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e7/8e7q ftp://data.pdbj.org/pub/pdb/validation_reports/e7/8e7q	HTTPS FTP

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Related structure data

Related structure data	8e7rC 8g7fC 8g7gC 8g7hC 8g7iC 4jh6S 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

Deposited unit

A: Metallothiol transferase FosB

B: Metallothiol transferase FosB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.314, 68.016, 69.802
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Metallothiol transferase FosB / Fosfomycin resistance protein Mass: 16488.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / NRS 248 / Gene: fosB, BCE_2111 / Production host: Escherichia coli (E. coli) References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups

#1: Protein

Metallothiol transferase FosB / Fosfomycin resistance protein

Mass: 16488.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus cereus (bacteria) / Strain: ATCC 10987 / NRS 248 / Gene: fosB, BCE_2111 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Non-polymers , 5 types, 225 molecules

#2: Chemical	ChemComp-UXR / (2S)-2-phosphonopropanoic acid Mass: 154.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇O₅P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG 3350, 125 mM magnesium formate, 5 mM 2-phosphonopropionic acid

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 24190 / % possible obs: 97.6 % / Redundancy: 5 % / R_merge(I) obs: 0.141 / R_pim(I) all: 0.069 / R_rim(I) all: 0.158 / Χ²: 0.665 / Net I/σ(I): 3.7 / Num. measured all: 121685

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	5.1	0.57	1182	0.775	0.274	0.634	0.492	98.3
1.93-1.97	5.2	0.488	1178	0.832	0.233	0.543	0.513	97.4
1.97-2.01	5.2	0.462	1196	0.861	0.22	0.513	0.494	97.5
2.01-2.05	5.2	0.392	1214	0.887	0.187	0.436	0.508	98.9
2.05-2.09	5.1	0.363	1168	0.899	0.175	0.405	0.517	97.3
2.09-2.14	5	0.327	1201	0.917	0.158	0.365	0.531	98
2.14-2.19	4.8	0.279	1151	0.93	0.139	0.313	0.538	95.2
2.19-2.25	5.2	0.255	1175	0.956	0.121	0.283	0.522	94.8
2.25-2.32	5.4	0.237	1216	0.956	0.11	0.261	0.507	98.3
2.32-2.39	5.4	0.22	1205	0.954	0.102	0.243	0.524	98.6
2.39-2.48	5.3	0.203	1213	0.97	0.095	0.225	0.518	98.8
2.48-2.58	5.2	0.19	1203	0.974	0.09	0.211	0.551	98.8
2.58-2.7	5.1	0.163	1234	0.979	0.078	0.181	0.58	98.9
2.7-2.84	4.9	0.147	1222	0.98	0.072	0.164	0.62	98.8
2.84-3.02	4.7	0.124	1212	0.985	0.063	0.14	0.666	98
3.02-3.25	4.3	0.102	1163	0.985	0.054	0.117	0.795	92.4
3.25-3.58	5	0.089	1229	0.989	0.044	0.1	0.906	98.5
3.58-4.09	4.9	0.075	1255	0.992	0.037	0.084	1.09	99.1
4.09-5.16	4.8	0.067	1255	0.993	0.034	0.075	1.144	98.4
5.16-50	4.7	0.084	1318	0.99	0.042	0.095	1.347	95.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	5.71 Å	38.83 Å
Translation	5.71 Å	38.83 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
HKL-2000		data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4JH6

4jh6

Resolution: 1.9→38.832 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.203 / WR_factor R_work: 0.158 / Average fsc free: 0.9678 / Average fsc work: 0.9798 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2188	1092	4.523 %	RANDOM
R_work	0.1693	23050	-	-
all	0.171	-	-	-
obs	-	24142	97.524 %	-

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: 17.204 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.005 Å²	-0 Å²	0 Å²
2-	-	-0.004 Å²	-0 Å²
3-	-	-	-0.001 Å²

Refinement step

Cycle: final / Resolution: 1.9→38.832 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2326	0	25	218	2569
B_iso mean	-	-	26.2	25.29	-
Num. residues	-	-	-	-	276

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2410
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2085
X-RAY DIFFRACTION	r_angle_refined_deg	1.489	1.64	3254
X-RAY DIFFRACTION	r_angle_other_deg	0.805	1.554	4864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.845	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.136	10	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.193	10	418
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.699	10	143
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	337
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2777
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	519
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	412
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	1953
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1125
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1170
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	179
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.076	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.076	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.229	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.732	1.697	1107
X-RAY DIFFRACTION	r_mcbond_other	1.72	1.696	1107
X-RAY DIFFRACTION	r_mcangle_it	2.568	2.534	1382
X-RAY DIFFRACTION	r_mcangle_other	2.567	2.536	1383
X-RAY DIFFRACTION	r_scbond_it	2.213	2.009	1303
X-RAY DIFFRACTION	r_scbond_other	2.212	2.009	1303
X-RAY DIFFRACTION	r_scangle_it	3.49	2.904	1872
X-RAY DIFFRACTION	r_scangle_other	3.489	2.905	1873
X-RAY DIFFRACTION	r_lrange_it	5.389	26.661	2717
X-RAY DIFFRACTION	r_lrange_other	5.291	26.226	2674

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
1.9-1.949	0.284	81	0.233	1678	0.235	1814	0.943	0.966	96.968	0.21
1.949-2.003	0.232	93	0.207	1603	0.209	1728	0.969	0.971	98.1481	0.185
2.003-2.061	0.243	77	0.194	1603	0.196	1708	0.963	0.975	98.3607	0.169
2.061-2.124	0.269	62	0.19	1583	0.193	1672	0.95	0.976	98.3852	0.164
2.124-2.193	0.214	59	0.178	1442	0.179	1576	0.976	0.98	95.2411	0.156
2.193-2.27	0.206	60	0.178	1458	0.179	1584	0.973	0.981	95.8333	0.157
2.27-2.355	0.229	65	0.156	1403	0.159	1486	0.964	0.984	98.7887	0.137
2.355-2.451	0.179	61	0.157	1377	0.158	1456	0.982	0.984	98.7637	0.136
2.451-2.56	0.194	53	0.165	1334	0.166	1408	0.975	0.983	98.5085	0.144
2.56-2.684	0.2	66	0.166	1254	0.168	1339	0.975	0.983	98.581	0.151
2.684-2.828	0.244	56	0.172	1192	0.175	1263	0.965	0.982	98.8124	0.157
2.828-2.999	0.212	63	0.169	1125	0.171	1212	0.975	0.982	98.0198	0.158
2.999-3.205	0.212	64	0.164	984	0.166	1142	0.972	0.983	91.7688	0.155
3.205-3.46	0.236	48	0.156	1007	0.16	1072	0.951	0.984	98.4142	0.15
3.46-3.787	0.242	46	0.151	941	0.155	995	0.963	0.986	99.196	0.147
3.787-4.229	0.18	22	0.14	867	0.141	899	0.981	0.988	98.8876	0.137
4.229-4.873	0.176	58	0.143	739	0.146	812	0.985	0.989	98.1527	0.148
4.873-5.945	0.249	37	0.181	623	0.184	684	0.975	0.986	96.4912	0.181
5.945-8.311	0.266	15	0.202	500	0.204	554	0.965	0.978	92.9603	0.208
8.311-38.832	0.16	6	0.178	337	0.178	347	0.993	0.967	98.8473	0.194

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