PDB-8xf7: High-resolution structure of the siderophore periplasmic binding ...

ID or keywords:

Entry

Database: PDB / ID: 8xf7

Title

High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine E bound

Components

Iron-hydroxamate ABC transporter substrate-binding protein FtsB

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: 1.12 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

-
Download

PDBx/mmCIF format	8xf7.cif.gz	192.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8xf7.ent.gz	115.6 KB	Display	PDB format
PDBx/mmJSON format	8xf7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/8xf7 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/8xf7	HTTPS FTP

-
Related structure data

Related structure data	8xetC 8xeuSC 8xf4C 8xf8C 8xf9C 8xfaC 8xfiC 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

-
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 FtsB

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	76.091, 76.091, 102.375
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

-
Protein , 1 types, 1 molecules A

#1: Protein	Iron-hydroxamate ABC transporter substrate-binding protein FtsB / FtsB Mass: 31849.482 Da / Num. of mol.: 1 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

-
Non-polymers , 7 types, 431 molecules

#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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.21 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350

-
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 2M / Detector: PIXEL / Date: May 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.12→40.42 Å / Num. obs: 128565 / % possible obs: 99.9 % / Redundancy: 18.6 % / CC_1/2: 0.75 / R_merge(I) obs: 0.047 / R_pim(I) all: 0.011 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.12→1.14 Å / Redundancy: 9.3 % / R_merge(I) obs: 0.961 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6276 / CC_1/2: 0.75 / R_pim(I) all: 0.326 / % possible all: 98.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS	Jan 10, 2022 BUILT=20220120	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: 1.12→40.42 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.98 / SU B: 0.663 / SU ML: 0.014 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.023
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1403	2634	2.05 %
R_work	0.1252	125853	-
all	0.126	-	-
obs	-	128487	99.943 %

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: 13.919 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.09 Å²	0.045 Å²	-0 Å²
2-	-	0.09 Å²	0 Å²
3-	-	-	-0.291 Å²

Refinement step

Cycle: LAST / Resolution: 1.12→40.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2222	0	59	421	2702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2384
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2346
X-RAY DIFFRACTION	r_angle_refined_deg	1.637	1.865	3232
X-RAY DIFFRACTION	r_angle_other_deg	0.561	1.805	5460
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.405	5	300
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.736	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.236	10	444
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.362	10	96
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	361
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2681
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	487
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	467
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	2146
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1175
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1156
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	248
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.096	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.208	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.165	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	36
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.028	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.101	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.693	1.34	1137
X-RAY DIFFRACTION	r_mcbond_other	2.683	1.339	1137
X-RAY DIFFRACTION	r_mcangle_it	4.007	2.419	1425
X-RAY DIFFRACTION	r_mcangle_other	4.016	2.421	1426
X-RAY DIFFRACTION	r_scbond_it	4.215	1.588	1247
X-RAY DIFFRACTION	r_scbond_other	4.214	1.589	1248
X-RAY DIFFRACTION	r_scangle_it	6.294	2.797	1796
X-RAY DIFFRACTION	r_scangle_other	6.293	2.797	1797
X-RAY DIFFRACTION	r_lrange_it	11.102	18.591	2900
X-RAY DIFFRACTION	r_lrange_other	9.801	15.981	2761
X-RAY DIFFRACTION	r_rigid_bond_restr	2.507	3	4730

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 (%)
1.12-1.149	0.217	173	0.194	9236	X-RAY DIFFRACTION	99.272
1.149-1.181	0.168	175	0.158	9045	X-RAY DIFFRACTION	100
1.181-1.215	0.147	198	0.133	8830	X-RAY DIFFRACTION	100
1.215-1.252	0.145	199	0.123	8493	X-RAY DIFFRACTION	100
1.252-1.293	0.136	147	0.114	8352	X-RAY DIFFRACTION	100
1.293-1.338	0.117	192	0.103	7982	X-RAY DIFFRACTION	100
1.338-1.389	0.127	179	0.095	7728	X-RAY DIFFRACTION	100
1.389-1.446	0.106	165	0.089	7430	X-RAY DIFFRACTION	99.9868
1.446-1.51	0.116	132	0.09	7174	X-RAY DIFFRACTION	99.9863
1.51-1.583	0.112	153	0.086	6850	X-RAY DIFFRACTION	100
1.583-1.669	0.103	111	0.088	6517	X-RAY DIFFRACTION	100
1.669-1.77	0.127	141	0.1	6146	X-RAY DIFFRACTION	100
1.77-1.892	0.135	111	0.106	5782	X-RAY DIFFRACTION	100
1.892-2.043	0.129	122	0.116	5381	X-RAY DIFFRACTION	100
2.043-2.237	0.127	107	0.113	5006	X-RAY DIFFRACTION	100
2.237-2.501	0.128	98	0.119	4458	X-RAY DIFFRACTION	100
2.501-2.886	0.173	80	0.141	3975	X-RAY DIFFRACTION	100
2.886-3.53	0.162	81	0.152	3368	X-RAY DIFFRACTION	100
3.53-4.973	0.155	40	0.143	2619	X-RAY DIFFRACTION	100
4.973-40.42	0.159	30	0.188	1481	X-RAY DIFFRACTION	100

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 7 types, 431 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 1 molecules A

-Non-polymers , 7 types, 431 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 7 types, 431 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi