PDB-8g7h: Crystal Structure of FosB from Bacillus cereus with Zinc and (1-h...

ID or keywords:

Entry

Database: PDB / ID: 8g7h

Title

Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxypropan-2-yl)phosphonic acid

Components

Metallothiol transferase FosB

Keywords

TRANSFERASE / FosB / inhibitor / homodimer / bacillithiol-S-transferase

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 / Resolution: 1.81 Å

Authors

Travis, S. / Pang, A.H. / 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	Feb 16, 2023	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 / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8g7h.cif.gz	83.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8g7h.ent.gz	59.1 KB	Display	PDB format
PDBx/mmJSON format	8g7h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8g7h_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8g7h_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8g7h_validation.xml.gz	15.7 KB	Display
Data in CIF	8g7h_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g7/8g7h ftp://data.pdbj.org/pub/pdb/validation_reports/g7/8g7h	HTTPS FTP

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Related structure data

Related structure data	8e7qC 8e7rC 8g7fC 8g7gC 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

33.9 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)	64.233, 68.210, 69.826
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) / 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) / 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 , 6 types, 284 molecules

#2: Chemical	ChemComp-YRQ / [(2S)-1-hydroxypropan-2-yl]phosphonic acid Mass: 140.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₉O₄P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 7 / 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: isolated from a natural source / Formula: Mg
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.29 Å³/Da / Density % sol: 46.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate ...Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate using a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen

Crystal

Density Matthews: 2.29 Å³/Da / Density % sol: 46.24 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate ...

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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: Sep 26, 2022

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.81→50 Å / Num. obs: 28683 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC_1/2: 0.994 / CC star: 0.999 / R_merge(I) obs: 0.138 / R_pim(I) all: 0.044 / R_rim(I) all: 0.145 / Χ²: 0.626 / Net I/σ(I): 4.1 / Num. measured all: 306631

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.81-1.84	9.5	0.785	1409	0.841	0.956	0.263	0.829	0.416	100
1.84-1.87	9.9	0.724	1411	0.856	0.96	0.238	0.763	0.439	99.9
1.87-1.91	10	0.646	1400	0.892	0.971	0.211	0.681	0.449	99.9
1.91-1.95	9.9	0.565	1432	0.907	0.975	0.187	0.596	0.491	99.8
1.95-1.99	9.3	0.484	1385	0.929	0.981	0.165	0.513	0.502	99.8
1.99-2.04	11.2	0.44	1407	0.954	0.988	0.137	0.461	0.525	100
2.04-2.09	11.4	0.403	1413	0.958	0.989	0.124	0.422	0.568	100
2.09-2.15	11.6	0.348	1423	0.966	0.991	0.107	0.364	0.553	100
2.15-2.21	11.4	0.305	1437	0.974	0.993	0.094	0.319	0.577	100
2.21-2.28	11.3	0.279	1400	0.977	0.994	0.087	0.293	0.612	99.9
2.28-2.36	11.2	0.236	1428	0.984	0.996	0.074	0.248	0.637	100
2.36-2.46	11.1	0.218	1417	0.983	0.996	0.068	0.229	0.623	99.9
2.46-2.57	10.8	0.198	1436	0.988	0.997	0.063	0.209	0.651	100
2.57-2.7	10.4	0.163	1438	0.99	0.997	0.053	0.171	0.677	99.9
2.7-2.87	9.4	0.127	1421	0.993	0.998	0.043	0.134	0.686	99.9
2.87-3.09	11.7	0.11	1442	0.995	0.999	0.034	0.115	0.78	100
3.09-3.41	11.6	0.09	1458	0.997	0.999	0.027	0.094	0.871	100
3.41-3.9	11.4	0.071	1462	0.998	0.999	0.022	0.074	0.921	99.9
3.9-4.91	10.7	0.054	1488	0.999	1	0.017	0.057	0.773	99.9
4.91-50	9.9	0.048	1576	0.999	1	0.016	0.051	0.618	99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
SCALEPACK	8.0.007	data scaling
PHASER	8.0.004	phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4JH6

4jh6

Resolution: 1.81→48.793 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1852	1462	5.107 %	RANDOM
R_work	0.1543	27164	-	-
all	0.156	-	-	-
obs	-	28626	99.725 %	-

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: 19.454 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.002 Å²	-0 Å²	-0 Å²
2-	-	-0.004 Å²	-0 Å²
3-	-	-	0.002 Å²

Refinement step

Cycle: LAST / Resolution: 1.81→48.793 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2324	0	47	270	2641

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2471
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2231
X-RAY DIFFRACTION	r_angle_refined_deg	1.52	1.659	3329
X-RAY DIFFRACTION	r_angle_other_deg	0.832	1.587	5136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.897	5	285
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.582	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.282	10	429
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.519	10	147
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	345
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2949
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	627
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	448
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	2121
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	1159
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1279
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	223
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.19	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.115	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.212	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.158	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	1.603	1.848	1127
X-RAY DIFFRACTION	r_mcbond_other	1.602	1.85	1128
X-RAY DIFFRACTION	r_mcangle_it	2.187	3.31	1412
X-RAY DIFFRACTION	r_mcangle_other	2.187	3.312	1413
X-RAY DIFFRACTION	r_scbond_it	2.835	2.273	1344
X-RAY DIFFRACTION	r_scbond_other	2.834	2.274	1345
X-RAY DIFFRACTION	r_scangle_it	4.495	3.965	1914
X-RAY DIFFRACTION	r_scangle_other	4.493	3.966	1915
X-RAY DIFFRACTION	r_lrange_it	6.454	25.528	2877
X-RAY DIFFRACTION	r_lrange_other	6.342	24.607	2802

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 (%)
1.81-1.855	0.287	128	0.267	1888	X-RAY DIFFRACTION	97.2504
1.855-1.906	0.213	90	0.213	1942	X-RAY DIFFRACTION	99.9508
1.906-1.961	0.183	98	0.182	1879	X-RAY DIFFRACTION	99.7477
1.961-2.021	0.176	115	0.165	1823	X-RAY DIFFRACTION	100
2.021-2.087	0.224	91	0.152	1760	X-RAY DIFFRACTION	100
2.087-2.16	0.185	79	0.145	1747	X-RAY DIFFRACTION	100
2.16-2.242	0.195	91	0.143	1646	X-RAY DIFFRACTION	100
2.242-2.333	0.168	88	0.134	1604	X-RAY DIFFRACTION	100
2.333-2.437	0.149	87	0.131	1547	X-RAY DIFFRACTION	100
2.437-2.555	0.186	97	0.139	1442	X-RAY DIFFRACTION	99.9351
2.555-2.693	0.211	82	0.148	1400	X-RAY DIFFRACTION	99.9326
2.693-2.856	0.161	72	0.152	1325	X-RAY DIFFRACTION	99.857
2.856-3.052	0.177	51	0.139	1282	X-RAY DIFFRACTION	100
3.052-3.296	0.175	61	0.149	1163	X-RAY DIFFRACTION	100
3.296-3.609	0.159	50	0.145	1114	X-RAY DIFFRACTION	100
3.609-4.032	0.187	57	0.137	984	X-RAY DIFFRACTION	100
4.032-4.65	0.148	53	0.122	877	X-RAY DIFFRACTION	99.7854
4.65-5.683	0.196	24	0.16	768	X-RAY DIFFRACTION	99.8739
5.683-7.983	0.246	35	0.207	600	X-RAY DIFFRACTION	99.686
7.983-48.793	0.201	13	0.223	373	X-RAY DIFFRACTION	98.2188

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