PDB-6wm7: Periplasmic EDTA-binding protein EppA, orthorhombic

ID or keywords:

Entry

Database: PDB / ID: 6wm7

Title

Periplasmic EDTA-binding protein EppA, orthorhombic

Components

Extracellular solute-binding protein, family 5

Keywords

PEPTIDE BINDING PROTEIN / Periplasmic binding protein /

EDTA /

bioremediation /

ABC transporter

Function / homology

Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport /

periplasmic space / Extracellular solute-binding protein, family 5

Function and homology information

Biological species

Chelativorans sp.

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Lewis, K.M. / Greene, C.L. / Sattler, S.A. / Xun, L. / Kang, C.

Funding support

United States, 1items

Citation

Journal: Int J Mol Sci / Year: 2020
Title: The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1.
Authors: Lewis, K.M. / Greene, C.L. / Sattler, S.A. / Youn, B. / Xun, L. / Kang, C.

History

Deposition	Apr 20, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wm7.cif.gz	618.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wm/6wm7 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wm7	HTTPS FTP

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Related structure data

Related structure data	6wm6C 1vr5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1bhs-1 1fdv-1 4oev-2 3dhe-1 1equ-d 6mne-d 6dtp-d 2grv-1 1fdt-1 7a0c-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Extracellular solute-binding protein, family 5

B: Extracellular solute-binding protein, family 5

hetero molecules

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

1

A: Extracellular solute-binding protein, family 5

hetero molecules

defined by author&software
Evidence: light scattering
63.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Extracellular solute-binding protein, family 5

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.339, 90.607, 165.266
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Extracellular solute-binding protein, family 5 Mass: 62560.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chelativorans sp. (strain BNC1) (bacteria) Strain: BNC1 / Gene: Meso_1835 / Production host: Escherichia coli (E. coli) / References: UniProt: Q11H97
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1285 / 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: 2.52 Å³/Da / Density % sol: 51.26 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 2.0 M ammonium sulfate

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.56→50 Å / Num. obs: 179522 / % possible obs: 99.8 % / Redundancy: 13.5 % / R_merge(I) obs: 0.125 / R_pim(I) all: 0.035 / R_rim(I) all: 0.13 / Χ²: 1 / Net I/σ(I): 7.9 / Num. measured all: 2422624

Reflection shell

Χ²: 1 / Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.56-1.57	3.6	1.608	4156	0.25	0.895	1.855	93.9
1.57-1.59	5.1	1.653	4423	0.311	0.779	1.837	99.3
1.59-1.6	6.9	1.583	4419	0.449	0.633	1.71	99.9
1.6-1.62	9.2	1.575	4481	0.55	0.537	1.666	100
1.62-1.63	11	1.524	4430	0.607	0.475	1.598	100
1.63-1.65	12.3	1.387	4450	0.682	0.408	1.447	100
1.65-1.66	13.3	1.364	4448	0.723	0.385	1.418	100
1.66-1.68	13.9	1.26	4471	0.775	0.348	1.308	100
1.68-1.7	14.2	1.111	4425	0.806	0.303	1.152	100
1.7-1.72	14.3	1.018	4487	0.848	0.277	1.055	100
1.72-1.74	14.4	0.95	4441	0.85	0.258	0.985	100
1.74-1.76	14.3	0.867	4463	0.872	0.236	0.899	100
1.76-1.78	14.4	0.748	4457	0.9	0.203	0.776	100
1.78-1.8	14.4	0.67	4452	0.922	0.182	0.695	100
1.8-1.82	14.4	0.587	4468	0.936	0.159	0.609	100
1.82-1.85	14.5	0.52	4480	0.946	0.141	0.539	100
1.85-1.88	14.4	0.46	4495	0.963	0.125	0.477	100
1.88-1.9	14.5	0.42	4433	0.967	0.114	0.436	100
1.9-1.93	14.5	0.354	4492	0.974	0.096	0.367	100
1.93-1.97	14.5	0.311	4456	0.981	0.084	0.322	100
1.97-2	14.5	0.271	4468	0.985	0.073	0.281	100
2-2.04	14.6	0.242	4465	0.988	0.065	0.25	100
2.04-2.07	14.6	0.22	4471	0.99	0.06	0.228	100
2.07-2.12	14.6	0.189	4492	0.992	0.051	0.196	100
2.12-2.16	14.6	0.174	4493	0.993	0.047	0.181	100
2.16-2.21	14.6	0.159	4489	0.994	0.043	0.165	100
2.21-2.27	14.6	0.153	4514	0.994	0.041	0.158	100
2.27-2.33	14.6	0.137	4450	0.996	0.037	0.142	100
2.33-2.4	14.6	0.127	4518	0.996	0.034	0.132	100
2.4-2.48	14.7	0.116	4513	0.997	0.031	0.12	100
2.48-2.56	14.6	0.105	4492	0.997	0.028	0.108	100
2.56-2.67	14.6	0.097	4503	0.998	0.026	0.1	100
2.67-2.79	14.6	0.093	4512	0.998	0.025	0.097	100
2.79-2.94	14.6	0.089	4553	0.998	0.024	0.093	100
2.94-3.12	14.6	0.082	4538	0.998	0.022	0.085	100
3.12-3.36	14.5	0.069	4566	0.998	0.019	0.071	100
3.36-3.7	14.3	0.055	4548	0.999	0.015	0.057	100
3.7-4.23	14	0.049	4601	0.999	0.014	0.051	100
4.23-5.33	14.6	0.046	4651	0.999	0.012	0.047	100
5.33-50	14.2	0.04	4858	0.999	0.011	0.042	100

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.15.2_3472	refinement
PHASER	2.8.2	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1vr5

1vr5

Resolution: 1.56→49.456 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.85

	R_factor	Num. reflection	% reflection
R_free	0.1707	1900	1.12 %
R_work	0.1522	-	-
obs	0.1524	169880	94.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 106.37 Å² / B_iso mean: 22.5481 Å² / B_iso min: 7.7 Å²

Refinement step

Cycle: final / Resolution: 1.56→49.456 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8256	0	215	1285	9756
B_iso mean	-	-	32.65	32.04	-
Num. residues	-	-	-	-	1070

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.5604-1.5994	0.3101	103	0.3286	9407	75
1.5994-1.6427	0.2646	129	0.2524	10671	85
1.6427-1.691	0.2015	111	0.211	11198	89
1.691-1.7456	0.2166	142	0.1914	11523	92
1.7456-1.808	0.2175	132	0.1727	11841	94
1.808-1.8804	0.2016	140	0.1574	12068	96
1.8804-1.966	0.194	129	0.1488	12296	97
1.966-2.0696	0.1533	151	0.1344	12398	98
2.0696-2.1993	0.1344	141	0.1302	12511	99
2.1993-2.3691	0.1464	135	0.132	12552	99
2.3691-2.6075	0.1477	152	0.1344	12657	99
2.6075-2.9848	0.1564	137	0.1406	12737	100
2.9848-3.7603	0.172	147	0.1416	12885	100
3.7603-49.456	0.1594	151	0.1484	13236	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	0.7396	0.2325	0.0019	0.3381	0.0449	0.2564	0.0082	-0.0452	-0.0178	0.0601	-0.0111	0.034	0.0272	-0.0354	0.0077	0.0989	-0.0088	0.004	0.1022	0.0148	0.0955	-24.2053	5.3019	-0.6509
2	0.6443	-0.2358	0.0938	0.7997	-0.009	0.2087	-0.0148	0.0302	0.0678	0.0208	-0.0175	-0.0413	-0.0429	-0.0287	-0.0353	0.0907	0.0019	-0.003	0.111	0.0148	0.0833	-30.8797	32.9034	-19.9605
3	0.1309	-0.0399	0.0184	0.2227	0.0456	0.2185	0.019	0.014	-0.0339	-0.002	-0.0229	0.0338	0.0185	-0.0261	-0	0.0877	-0.0046	-0.0017	0.1099	0.0049	0.0979	-28.7251	14.3655	-15.3974
4	0.5836	0.2679	0.0199	0.623	0.0047	0.3658	-0.0208	0.1187	-0.0686	-0.0561	0.013	-0.0507	0.0633	-0.0025	-0.0179	0.124	-0.0132	0.0046	0.1157	-0.0247	0.1069	-17.6243	-2.178	-40.429
5	0.7603	-0.5353	-0.036	0.8638	-0.36	0.1283	0.0018	0.0109	0.0328	-0.0642	-0.0701	-0.0379	0.0771	0.0382	-0.0145	0.146	0.0238	-0.008	0.1067	-0.0017	0.1242	6.1669	-14.2133	-21.8866
6	0.2994	-0.0894	0.0077	0.1114	-0.02	0.1306	-0.0139	0.0395	-0.0166	-0.0176	0.004	-0.0079	0.0371	0.0227	0	0.1252	-0.0042	-0.0069	0.0977	-0.009	0.1205	-10.189	-2.2241	-26.3578

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 301 )	A	31 - 301
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 302 through 465 )	A	302 - 465
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 466 through 564 )	A	466 - 564
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 31 through 301 )	B	31 - 301
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 302 through 490 )	B	302 - 490
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 491 through 566 )	B	491 - 566

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