PDB-8g7g: Crystal Structure of FosB from Bacillus cereus with Zinc and (1-h...

ID or keywords:

Entry

Database: PDB / ID: 8g7g

Title

Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxy-2-methylpropyl)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: 2.23 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	8g7g.cif.gz	80.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8g7g_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8g7g_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8g7g_validation.xml.gz	14.5 KB	Display
Data in CIF	8g7g_validation.cif.gz	20.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g7/8g7g ftp://data.pdbj.org/pub/pdb/validation_reports/g7/8g7g	HTTPS FTP

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Related structure data

Related structure data	8e7qC 8e7rC 8g7fC 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)	64.234, 68.534, 69.541
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 , 5 types, 183 molecules

#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-YS8 / [(1R)-1-hydroxy-2-methylpropyl]phosphonic acid Mass: 154.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₁O₄P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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.: 176 / 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: 2.28 Å³/Da / Density % sol: 45.95 %
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 (50 mM Mg formate and 16% (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 (50 mM Mg formate and 16% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate with a 1:1 ratio of each solution. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen.

Crystal

Density Matthews: 2.28 Å³/Da / Density % sol: 45.95 %

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 (50 mM Mg formate and 16% (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: Jun 15, 2015

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.23→50 Å / Num. obs: 15452 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC_1/2: 0.986 / CC star: 0.996 / R_merge(I) obs: 0.144 / R_pim(I) all: 0.055 / R_rim(I) all: 0.154 / Χ²: 0.568 / Net I/σ(I): 4.2 / Num. measured all: 121114

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
2.23-2.27	6.6	0.552	738	0.845	0.957	0.226	0.6	0.583	98.5
2.27-2.31	6.9	0.505	750	0.817	0.948	0.204	0.547	0.52	97.9
2.31-2.35	7.3	0.485	749	0.863	0.963	0.194	0.524	0.495	99.3
2.35-2.4	7.5	0.45	753	0.888	0.97	0.177	0.485	0.528	99.5
2.4-2.45	7.8	0.466	761	0.885	0.969	0.18	0.501	0.475	99.7
2.45-2.51	7.7	0.432	752	0.945	0.986	0.168	0.465	0.488	99.9
2.51-2.57	7	0.361	776	0.928	0.981	0.147	0.391	0.513	99.9
2.57-2.64	8.1	0.332	759	0.951	0.987	0.126	0.355	0.504	100
2.64-2.72	8.4	0.3	752	0.944	0.985	0.111	0.32	0.543	100
2.72-2.81	8.7	0.267	761	0.965	0.991	0.097	0.285	0.535	100
2.81-2.91	8.6	0.221	781	0.976	0.994	0.081	0.236	0.552	100
2.91-3.03	8.5	0.203	772	0.982	0.996	0.075	0.216	0.573	100
3.03-3.16	8.3	0.157	773	0.987	0.997	0.058	0.168	0.641	100
3.16-3.33	8.3	0.137	768	0.989	0.997	0.051	0.147	0.685	99.7
3.33-3.54	7.8	0.114	771	0.991	0.998	0.044	0.122	0.695	99.7
3.54-3.81	7	0.085	778	0.994	0.998	0.034	0.092	0.707	99.9
3.81-4.2	8.5	0.072	779	0.997	0.999	0.026	0.077	0.672	100
4.2-4.8	8.5	0.054	792	0.999	1	0.02	0.057	0.605	99.9
4.8-6.05	8.1	0.053	817	0.999	1	0.02	0.057	0.515	100
6.05-50	7.2	0.042	870	0.999	1	0.017	0.046	0.513	99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
HKL-2000		data scaling
PHASER	8.0.004	phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4JH6

4jh6

Resolution: 2.23→47.185 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2461	756	4.907 %	RANDOM
R_work	0.1773	14649	-	-
all	0.181	-	-	-
obs	-	15405	99.048 %	-

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: 22.768 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.003 Å²	0 Å²	0 Å²
2-	-	0.004 Å²	0 Å²
3-	-	-	-0.001 Å²

Refinement step

Cycle: LAST / Resolution: 2.23→47.185 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2324	0	25	176	2525

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	2460
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2224
X-RAY DIFFRACTION	r_angle_refined_deg	1.514	1.661	3326
X-RAY DIFFRACTION	r_angle_other_deg	0.813	1.582	5117
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.591	5	286
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.126	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.2	10	429
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.163	10	147
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	344
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2952
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	628
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	428
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	2032
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1120
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1216
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	160
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.076	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.087	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.085	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.534	2.255	1132
X-RAY DIFFRACTION	r_mcbond_other	1.534	2.255	1132
X-RAY DIFFRACTION	r_mcangle_it	2.373	4.07	1422
X-RAY DIFFRACTION	r_mcangle_other	2.372	4.07	1423
X-RAY DIFFRACTION	r_scbond_it	2.201	2.564	1328
X-RAY DIFFRACTION	r_scbond_other	2.189	2.564	1326
X-RAY DIFFRACTION	r_scangle_it	3.618	4.58	1904
X-RAY DIFFRACTION	r_scangle_other	3.617	4.58	1905
X-RAY DIFFRACTION	r_lrange_it	5.193	24.349	2724
X-RAY DIFFRACTION	r_lrange_other	5.178	24.15	2683

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 (%)
2.23-2.286	0.299	44	0.226	990	X-RAY DIFFRACTION	90.4637
2.286-2.348	0.298	55	0.229	1012	X-RAY DIFFRACTION	98.7049
2.348-2.416	0.256	56	0.211	1003	X-RAY DIFFRACTION	99.4366
2.416-2.49	0.282	58	0.211	983	X-RAY DIFFRACTION	99.7126
2.49-2.572	0.324	54	0.205	961	X-RAY DIFFRACTION	99.9016
2.572-2.662	0.263	46	0.188	926	X-RAY DIFFRACTION	100
2.662-2.762	0.264	58	0.175	878	X-RAY DIFFRACTION	100
2.762-2.874	0.294	50	0.167	866	X-RAY DIFFRACTION	100
2.874-3.002	0.263	36	0.178	833	X-RAY DIFFRACTION	100
3.002-3.148	0.289	38	0.176	815	X-RAY DIFFRACTION	100
3.148-3.317	0.257	25	0.173	767	X-RAY DIFFRACTION	99.8739
3.317-3.517	0.25	36	0.159	724	X-RAY DIFFRACTION	99.7375
3.517-3.758	0.222	27	0.154	695	X-RAY DIFFRACTION	99.8617
3.758-4.057	0.187	30	0.146	642	X-RAY DIFFRACTION	100
4.057-4.441	0.164	30	0.13	588	X-RAY DIFFRACTION	100
4.441-4.96	0.162	39	0.129	531	X-RAY DIFFRACTION	99.8249
4.96-5.717	0.336	11	0.166	499	X-RAY DIFFRACTION	100
5.717-6.976	0.308	30	0.241	408	X-RAY DIFFRACTION	99.5455
6.976-9.76	0.226	22	0.201	323	X-RAY DIFFRACTION	99.1379
9.76-47.185	0.195	11	0.308	205	X-RAY DIFFRACTION	98.1818

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