PDB-8xfi: High-resolution structure of the siderophore periplasmic binding ...

ID or keywords:

Entry

Database: PDB / ID: 8xfi

Title

High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine E bound (crystal form 2)

Components

Iron-hydroxamate ABC transporter substrate-binding protein

Keywords

METAL BINDING PROTEIN / Streptococcus pyogenes / siderophore / hydroxamate / FtsB / ABC transporter / alanine scanning / antibiotic strategy / ferrioxamine E

Function / homology

Function and homology information

iron coordination entity transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function

Biological species

Streptococcus pyogenes SSI-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Caaveiro, J.M.M. / Fernandez-Perez, J. / Tsumoto, K.

Funding support

Japan, 1items

Citation

Journal: Structure / Year: 2024
Title: Structural basis for the ligand promiscuity of the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes.
Authors: Fernandez-Perez, J. / Senoo, A. / Caaveiro, J.M.M. / Nakakido, M. / de Vega, S. / Nakagawa, I. / Tsumoto, K.

History

Deposition	Dec 13, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Dec 18, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8xfi.cif.gz	302.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8xfi.ent.gz	187.8 KB	Display	PDB format
PDBx/mmJSON format	8xfi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8xfi_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8xfi_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8xfi_validation.xml.gz	27.7 KB	Display
Data in CIF	8xfi_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/8xfi ftp://data.pdbj.org/pub/pdb/validation_reports/xf/8xfi	HTTPS FTP

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Related structure data

Related structure data	8xetC 8xeuSC 8xf4C 8xf7C 8xf8C 8xf9C 8xfaC 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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Iron-hydroxamate ABC transporter substrate-binding protein

B: Iron-hydroxamate ABC transporter substrate-binding protein

hetero molecules

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

1

A: Iron-hydroxamate ABC transporter substrate-binding protein

hetero molecules

defined by author
Evidence: gel filtration
32.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Iron-hydroxamate ABC transporter substrate-binding protein

hetero molecules

defined by author
32.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.415, 70.571, 69.073
Angle α, β, γ (deg.)	90.000, 110.658, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Iron-hydroxamate ABC transporter substrate-binding protein / FtsB Mass: 31849.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes SSI-1 (bacteria) Gene: E0F66_02370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5S4TPK8
#2: Chemical	ChemComp-6L0 / (8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone Mass: 598.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₄₆N₆O₉ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.2 Å³/Da / Density % sol: 44.06 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 100 mM BIS-TRIS pH 5.5 200 mM Magnesium choride 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→47.7 Å / Num. obs: 40353 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.042 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.95→2 Å / R_merge(I) obs: 0.883 / Mean I/σ(I) obs: 2 / Num. unique obs: 2812 / CC_1/2: 0.73 / R_pim(I) all: 0.379

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS	Feb 5, 2021 BUILT=20210323	data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8XEU

8xeu

Resolution: 1.95→47.7 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.94 / SU B: 8.328 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2322	2075	5.144 %
R_work	0.1915	38261	-
all	0.194	-	-
obs	-	40336	99.864 %

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: 32.228 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.17 Å²	-0 Å²	-0.273 Å²
2-	-	0.606 Å²	-0 Å²
3-	-	-	-0.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→47.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4372	0	88	216	4676

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	4563
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4468
X-RAY DIFFRACTION	r_angle_refined_deg	1.574	1.863	6167
X-RAY DIFFRACTION	r_angle_other_deg	0.533	1.803	10365
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.778	5	551
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.472	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.015	10	830
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.93	10	182
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	687
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5103
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	937
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	888
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	4031
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2275
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2287
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	207
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.004	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.068	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.118	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.158	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.039	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.398	2.012	2198
X-RAY DIFFRACTION	r_mcbond_other	1.396	2.012	2198
X-RAY DIFFRACTION	r_mcangle_it	2.092	3.61	2745
X-RAY DIFFRACTION	r_mcangle_other	2.092	3.611	2746
X-RAY DIFFRACTION	r_scbond_it	2.179	2.351	2365
X-RAY DIFFRACTION	r_scbond_other	2.179	2.351	2366
X-RAY DIFFRACTION	r_scangle_it	3.513	4.173	3420
X-RAY DIFFRACTION	r_scangle_other	3.512	4.173	3421
X-RAY DIFFRACTION	r_lrange_it	4.69	21.254	5180
X-RAY DIFFRACTION	r_lrange_other	4.68	21.129	5155

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 (%)
1.95-2.001	0.291	158	0.26	2798	X-RAY DIFFRACTION	99.7637
2.001-2.055	0.291	170	0.235	2739	X-RAY DIFFRACTION	100
2.055-2.115	0.274	134	0.219	2674	X-RAY DIFFRACTION	99.9288
2.115-2.18	0.265	133	0.216	2598	X-RAY DIFFRACTION	100
2.18-2.251	0.299	129	0.216	2517	X-RAY DIFFRACTION	100
2.251-2.33	0.254	128	0.203	2451	X-RAY DIFFRACTION	99.9612
2.33-2.418	0.268	122	0.199	2328	X-RAY DIFFRACTION	100
2.418-2.516	0.232	126	0.191	2256	X-RAY DIFFRACTION	100
2.516-2.628	0.248	116	0.196	2179	X-RAY DIFFRACTION	99.9564
2.628-2.755	0.279	132	0.21	2064	X-RAY DIFFRACTION	99.909
2.755-2.904	0.267	98	0.199	1987	X-RAY DIFFRACTION	99.8563
2.904-3.079	0.277	98	0.225	1880	X-RAY DIFFRACTION	99.899
3.079-3.291	0.244	89	0.223	1760	X-RAY DIFFRACTION	99.892
3.291-3.553	0.252	94	0.212	1619	X-RAY DIFFRACTION	99.593
3.553-3.89	0.219	100	0.174	1490	X-RAY DIFFRACTION	99.3129
3.89-4.346	0.154	60	0.139	1380	X-RAY DIFFRACTION	99.5162
4.346-5.011	0.158	63	0.134	1211	X-RAY DIFFRACTION	99.6091
5.011-6.121	0.158	50	0.171	1049	X-RAY DIFFRACTION	99.8184
6.121-8.586	0.195	55	0.168	800	X-RAY DIFFRACTION	100
8.586-47.7	0.23	20	0.189	481	X-RAY DIFFRACTION	100

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	3.0428	0.0707	1.3188	0.4778	0.1877	1.5631	0.0466	0.2218	0.0311	-0.017	-0.0175	-0.0212	0.0761	0.1459	-0.0292	0.0987	0.008	0.0509	0.0737	0.0092	0.05	-20.081	16.0247	-24.0736
2	2.6847	-0.1267	0.8247	0.5876	0.0188	1.0991	0.0555	-0.1299	-0.0705	0.0547	-0.0138	-0.0002	0.0401	-0.0436	-0.0417	0.0568	-0.0004	0.0473	0.0092	0.0096	0.0534	-34.1798	12.3123	4.9585

Refinement TLS group

Selection: ALL

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