PDB-7atr: The Crystal Structure of YejA - an ABC Peptide Transporter Receptor

ID or keywords:

Entry

Database: PDB / ID: 7atr

Title

The Crystal Structure of YejA - an ABC Peptide Transporter Receptor

Components

(Uncharacterized protein YejA) x 2

Keywords

PEPTIDE BINDING PROTEIN / Peptide-uptake Antimicrobial peptide ABC transporter

Function / homology

Function and homology information

microcin transport / oligopeptide transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Ackroyd, B.K. / Dodson, E.J. / Wilkinson, A.J. / Thomas, G.T.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: The Crystal Structure of YejA - an ABC Peptide Transporter Receptor
Authors: Ackroyd, B.K. / Dodson, E.J. / Wilkinson, A.J. / Thomas, G.H.

History

Deposition	Oct 30, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7atr.cif.gz	252.5 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7atr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7atr_validation.pdf.gz	438.2 KB	Display	wwPDB validaton report
Full document	7atr_full_validation.pdf.gz	439.5 KB	Display
Data in XML	7atr_validation.xml.gz	25.9 KB	Display
Data in CIF	7atr_validation.cif.gz	38.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/at/7atr ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atr	HTTPS FTP

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Related structure data

Related structure data	4onyS S: Starting model for refinement
Similar structure data	6a1e-d 2wgf-4 3fec-d 4ku5-d 2wge-1 2wgd-1 4m2e-1 2jkp-1 3fk5-2 4c71-d Search similar-shape structures by Omokage search (details) 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: Uncharacterized protein YejA

B: Uncharacterized protein YejA

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, SEC-MALLS

Unit cell

Length a, b, c (Å)	91.440, 105.267, 145.387
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#1: Protein	Uncharacterized protein YejA Mass: 67124.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chain A is a conventional peptide binding protein component of an ABC uptake system in bacteria. Chain B is a peptide derived from this protein which is a found as a ligand in this protein. Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yejA, b2177, JW2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33913
#2: Protein/peptide	Uncharacterized protein YejA Mass: 1328.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chain A is a conventional peptide binding protein component of an ABC uptake system in bacteria. Chain B is a peptide derived from this protein which is a found as a ligand in this protein. Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: yejA, b2177, JW2165 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.57 Å³/Da / Density % sol: 52.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0 Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5 Drops: 300 nl (150 nl ...Details: Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0 Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5 Drops: 300 nl (150 nl protein solution + 150 nl reservoir solution) Reservoir: 100 microlitres

Crystal

Density Matthews: 2.57 Å³/Da / Density % sol: 52.1 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0 Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5 Drops: 300 nl (150 nl ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.92819 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.92819 Å / Relative weight: 1

Reflection

Resolution: 1.55→85.264 Å / Num. obs: 101011 / % possible obs: 99.6 % / Redundancy: 8.4 % / B_iso Wilson estimate: 15.46 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.038 / R_rim(I) all: 0.08 / Net I/σ(I): 14.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.49-85.26	7.8	0.034	36.9	702	0.956	0.018	0.039
1.55-1.58	8.5	0.668	2.4	4874	0.904	0.353	0.756

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data processing
Aimless	0.7.4	data reduction
Aimless	0.7.4	data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ONY

4ony

Resolution: 1.55→85.264 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.967 / SU B: 1.318 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1846	4874	4.825 %
R_work	0.1701	96135	-
all	0.171	-	-
obs	-	101009	99.528 %

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: 20.793 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.846 Å²	0 Å²	-0 Å²
2-	-	-0.539 Å²	0 Å²
3-	-	-	-1.307 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→85.264 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4841	0	18	408	5267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	5073
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4663
X-RAY DIFFRACTION	r_angle_refined_deg	1.827	1.649	6907
X-RAY DIFFRACTION	r_angle_other_deg	1.455	1.582	10708
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.791	5	605
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.24	21.779	298
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.952	15	814
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.618	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	625
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5833
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1309
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	759
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	3712
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2289
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2016
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	193
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.149	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.173	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.283	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.632	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.863	1.929	2402
X-RAY DIFFRACTION	r_mcbond_other	1.839	1.927	2401
X-RAY DIFFRACTION	r_mcangle_it	2.639	2.887	3013
X-RAY DIFFRACTION	r_mcangle_other	2.638	2.888	3014
X-RAY DIFFRACTION	r_scbond_it	3.283	2.238	2671
X-RAY DIFFRACTION	r_scbond_other	3.282	2.241	2672
X-RAY DIFFRACTION	r_scangle_it	4.862	3.218	3894
X-RAY DIFFRACTION	r_scangle_other	4.862	3.22	3895
X-RAY DIFFRACTION	r_lrange_it	5.839	21.937	5437
X-RAY DIFFRACTION	r_lrange_other	5.749	21.718	5387

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
1.55-1.59	0.263	349	0.237	6980	0.238	7411	0.868	0.877	98.8935	0.229
1.59-1.634	0.243	348	0.218	6826	0.219	7240	0.895	0.9	99.0884	0.207
1.634-1.681	0.225	353	0.199	6616	0.2	7044	0.91	0.923	98.9353	0.187
1.681-1.733	0.212	349	0.188	6458	0.189	6869	0.932	0.935	99.0974	0.175
1.733-1.79	0.219	351	0.171	6240	0.173	6639	0.935	0.946	99.277	0.158
1.79-1.852	0.205	284	0.166	6119	0.168	6441	0.936	0.952	99.41	0.154
1.852-1.922	0.202	272	0.163	5901	0.164	6204	0.946	0.955	99.5003	0.151
1.922-2.001	0.186	277	0.157	5690	0.158	5990	0.955	0.963	99.616	0.147
2.001-2.09	0.179	270	0.164	5481	0.165	5769	0.959	0.963	99.688	0.157
2.09-2.192	0.179	274	0.163	5238	0.164	5526	0.963	0.965	99.7467	0.157
2.192-2.31	0.181	252	0.165	4943	0.166	5205	0.962	0.965	99.8079	0.159
2.31-2.45	0.171	230	0.159	4743	0.16	4980	0.966	0.967	99.8594	0.156
2.45-2.619	0.185	219	0.162	4423	0.163	4644	0.963	0.964	99.9569	0.161
2.619-2.829	0.171	213	0.159	4174	0.16	4389	0.962	0.965	99.9544	0.16
2.829-3.098	0.189	195	0.167	3835	0.168	4030	0.957	0.962	100	0.171
3.098-3.464	0.194	179	0.168	3485	0.169	3664	0.959	0.965	100	0.176
3.464-3.998	0.167	168	0.163	3070	0.163	3238	0.968	0.969	100	0.176
3.998-4.894	0.147	140	0.145	2610	0.145	2750	0.981	0.979	100	0.165
4.894-6.91	0.207	92	0.217	2092	0.216	2184	0.962	0.967	100	0.24
6.91-85.264	0.155	59	0.196	1211	0.194	1271	0.981	0.97	99.9213	0.264

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