PDB-7ath: Crystal structure of UipA

ID or keywords:

Entry

Database: PDB / ID: 7ath

Title

Crystal structure of UipA

Components

UipA

Keywords

METAL BINDING PROTEIN / Native / membrane protein / metal binding

Function / homology

membrane / PepSY domain-containing protein

Function and homology information

Biological species

Microbacterium sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.343 Å

Authors

Bremond, N. / Gallois, N. / Legrand, P. / Chapon, V. / Arnoux, P.

Funding support

France, 1items

Citation

Journal: Isme J / Year: 2022
Title: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria.
Authors: Gallois, N. / Alpha-Bazin, B. / Bremond, N. / Ortet, P. / Barakat, M. / Piette, L. / Mohamad Ali, A. / Lemaire, D. / Legrand, P. / Theodorakopoulos, N. / Floriani, M. / Fevrier, L. / Den ...

History

Deposition	Oct 30, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Jun 19, 2024	Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ath.cif.gz	42.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7ath.ent.gz		Display	PDB format
PDBx/mmJSON format	7ath.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ath_validation.pdf.gz	424.9 KB	Display	wwPDB validaton report
Full document	7ath_full_validation.pdf.gz	425.4 KB	Display
Data in XML	7ath_validation.xml.gz	7.2 KB	Display
Data in CIF	7ath_validation.cif.gz	8.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/at/7ath ftp://data.pdbj.org/pub/pdb/validation_reports/at/7ath	HTTPS FTP

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Related structure data

Related structure data	7atkC C: citing same article (ref.)
Similar structure data	7atk-1 5sxg-d 6rnx-d 2f4w-d 2bq4-d 4u68-d 3f81-d 3h5e-d 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

AAA: UipA

hetero molecules

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

1

AAA: UipA

hetero molecules

AAA: UipA

hetero molecules

defined by author&software
Evidence: gel filtration, monomer in solution at relatively low protein concentration
43.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.130, 96.130, 52.550
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-304- ZN

#1: Protein	UipA Mass: 21389.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium sp. (bacteria) / Gene: CVS53_03692 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9JIL7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.84 Å³/Da / Density % sol: 56.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: MES pH6 100mM, PEG6K 22%, ZnCl2 5-15mM Formamide 6%

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 2.2→43 Å / Num. obs: 23892 / % possible obs: 99.8 % / Redundancy: 14 % / CC_1/2: 0.99 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.2→2.33 Å / Num. unique obs: 3813 / CC_1/2: 0.53

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.343→42.991 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.959 / SU B: 7.159 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.182
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2474	540	5.004 %
R_work	0.2184	10251	-
all	0.22	-	-
obs	-	10791	99.741 %

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: 71.975 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.236 Å²	0 Å²	0 Å²
2-	-	-2.236 Å²	0 Å²
3-	-	-	4.472 Å²

Refinement step

Cycle: LAST / Resolution: 2.343→42.991 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	962	0	5	8	975

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	967
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	883
X-RAY DIFFRACTION	r_angle_refined_deg	1.842	1.629	1322
X-RAY DIFFRACTION	r_angle_other_deg	1.408	1.588	2038
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.228	5	134
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.297	24.783	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.168	15	141
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.187	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	149
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1130
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	177
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	162
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	739
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	473
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	481
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.218	0.2	15
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.035	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.284	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.408	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.117	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.009	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.405	7.444	542
X-RAY DIFFRACTION	r_mcbond_other	6.405	7.443	541
X-RAY DIFFRACTION	r_mcangle_it	9.173	11.139	674
X-RAY DIFFRACTION	r_mcangle_other	9.169	11.141	675
X-RAY DIFFRACTION	r_scbond_it	9.194	8.125	425
X-RAY DIFFRACTION	r_scbond_other	9.185	8.129	426
X-RAY DIFFRACTION	r_scangle_it	12.535	11.868	648
X-RAY DIFFRACTION	r_scangle_other	12.525	11.873	649
X-RAY DIFFRACTION	r_lrange_it	14.878	88.612	950
X-RAY DIFFRACTION	r_lrange_other	14.871	88.66	951

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
2.343-2.403	0.407	38	0.365	712	0.367	773	0.85	0.816	97.0246	0.349
2.403-2.469	0.344	37	0.344	722	0.344	759	0.858	0.815	100	0.32
2.469-2.54	0.372	37	0.29	700	0.294	737	0.803	0.856	100	0.256
2.54-2.618	0.44	36	0.306	683	0.312	719	0.788	0.852	100	0.274
2.618-2.704	0.456	35	0.286	655	0.294	690	0.836	0.881	100	0.25
2.704-2.798	0.3	34	0.273	651	0.274	685	0.872	0.871	100	0.244
2.798-2.903	0.3	33	0.282	623	0.283	656	0.839	0.85	100	0.246
2.903-3.021	0.303	31	0.272	601	0.273	632	0.877	0.867	100	0.242
3.021-3.155	0.368	31	0.264	575	0.268	606	0.829	0.884	100	0.241
3.155-3.308	0.303	30	0.235	566	0.239	596	0.9	0.915	100	0.222
3.308-3.486	0.302	27	0.224	514	0.228	541	0.904	0.928	100	0.214
3.486-3.696	0.275	26	0.224	508	0.226	534	0.931	0.945	100	0.218
3.696-3.949	0.178	25	0.199	471	0.198	496	0.961	0.955	100	0.2
3.949-4.262	0.181	24	0.173	445	0.173	469	0.957	0.969	100	0.18
4.262-4.665	0.162	21	0.142	413	0.143	434	0.981	0.976	100	0.153
4.665-5.208	0.201	21	0.164	388	0.166	409	0.963	0.965	100	0.175
5.208-5.999	0.22	17	0.23	336	0.23	353	0.955	0.938	100	0.243
5.999-7.311	0.258	16	0.239	298	0.24	314	0.944	0.94	100	0.259
7.311-10.193	0.2	12	0.165	236	0.166	248	0.972	0.973	100	0.196
10.193-42.991	0.264	9	0.285	154	0.284	165	0.976	0.938	98.7879	0.334

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