PDB-7l22: Structure of chloride soak form of ArrX from Chrysiogenes arsenatis

ID or keywords:

Entry

Database: PDB / ID: 7l22

Title

Structure of chloride soak form of ArrX from Chrysiogenes arsenatis

Components

ArrX

Keywords

SIGNALING PROTEIN / Periplasmic binding protein

Biological species

Chrysiogenes arsenatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.925 Å

Authors

Maher, M.J. / Poddar, N.

Citation

Journal: Biochemistry / Year: 2021
Title: Structural and Functional Investigation of the Periplasmic Arsenate-Binding Protein ArrX from Chrysiogenes arsenatis .
Authors: Poddar, N. / Badilla, C. / Maghool, S. / Osborne, T.H. / Santini, J.M. / Maher, M.J.

History

Deposition	Dec 16, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 24, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	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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Download

PDBx/mmCIF format	7l22.cif.gz	71.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7l22.ent.gz	49.3 KB	Display	PDB format
PDBx/mmJSON format	7l22.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7l22_validation.pdf.gz	872.4 KB	Display	wwPDB validaton report
Full document	7l22_full_validation.pdf.gz	874.1 KB	Display
Data in XML	7l22_validation.xml.gz	12.2 KB	Display
Data in CIF	7l22_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/7l22 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/7l22	HTTPS FTP

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Related structure data

Related structure data	6x6bSC 6x8wC 6x9gC 6xabC 6xadC 6xl2C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6x8w-d 6x9g-d 6x6b-d 3daj-d 5lq1-1 6eu7-1 4zjr-3 1ol6-d 6xab-d 5aaf-d Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ArrX

hetero molecules

34.4 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)	52.896, 54.477, 90.844
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ArrX Mass: 34338.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chrysiogenes arsenatis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium chloride, 0.1 M Tris pH 8.5, 27% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 1.92→46.72 Å / Num. obs: 20389 / % possible obs: 99 % / Redundancy: 20 % / CC_1/2: 1 / Net I/σ(I): 20
Reflection shell	Resolution: 1.92→1.97 Å / Num. unique obs: 1173 / CC_1/2: 0.857

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6X6B

6x6b

Resolution: 1.925→46.72 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.21 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2135	1002	4.926 %
R_work	0.1685	19340	-
all	0.171	-	-
obs	-	20342	98.983 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 39.424 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.5 Å²	0 Å²	0 Å²
2-	-	4.997 Å²	0 Å²
3-	-	-	-2.497 Å²

Refinement step

Cycle: LAST / Resolution: 1.925→46.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2023	0	5	98	2126

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2151
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2017
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	1.645	2937
X-RAY DIFFRACTION	r_angle_other_deg	1.326	1.566	4671
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.792	5	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.82	20.645	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.171	15	366
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.763	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	281
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2443
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	492
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	436
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	1905
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1048
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	957
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.213	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.136	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.544	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.679	3.856	1048
X-RAY DIFFRACTION	r_mcbond_other	2.676	3.854	1047
X-RAY DIFFRACTION	r_mcangle_it	3.603	5.77	1315
X-RAY DIFFRACTION	r_mcangle_other	3.602	5.774	1316
X-RAY DIFFRACTION	r_scbond_it	4.173	4.43	1103
X-RAY DIFFRACTION	r_scbond_other	4.171	4.434	1100
X-RAY DIFFRACTION	r_scangle_it	6.335	6.442	1610
X-RAY DIFFRACTION	r_scangle_other	6.343	6.448	1605
X-RAY DIFFRACTION	r_lrange_it	8.371	46.524	2422
X-RAY DIFFRACTION	r_lrange_other	8.335	46.307	2400

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
1.925-1.974	0.278	71	0.267	1223	0.268	1495	0.759	0.743	86.5552	0.231
1.974-2.028	0.289	72	0.246	1384	0.248	1456	0.772	0.766	100	0.213
2.028-2.087	0.234	63	0.228	1336	0.229	1400	0.791	0.83	99.9286	0.202
2.087-2.151	0.213	71	0.192	1313	0.193	1384	0.9	0.9	100	0.166
2.151-2.222	0.217	77	0.183	1247	0.185	1324	0.911	0.921	100	0.161
2.222-2.299	0.245	55	0.18	1252	0.183	1307	0.916	0.924	100	0.159
2.299-2.386	0.197	54	0.168	1193	0.17	1247	0.938	0.941	100	0.148
2.386-2.483	0.247	68	0.154	1129	0.158	1198	0.923	0.955	99.9165	0.136
2.483-2.593	0.207	66	0.154	1097	0.157	1163	0.939	0.958	100	0.136
2.593-2.719	0.189	42	0.17	1068	0.171	1111	0.952	0.953	99.91	0.152
2.719-2.866	0.226	55	0.16	996	0.163	1051	0.942	0.957	100	0.146
2.866-3.039	0.222	51	0.152	964	0.155	1017	0.936	0.963	99.8033	0.141
3.039-3.248	0.17	51	0.166	882	0.166	933	0.953	0.959	100	0.155
3.248-3.507	0.195	40	0.161	860	0.162	900	0.96	0.96	100	0.151
3.507-3.839	0.23	47	0.158	773	0.162	820	0.943	0.961	100	0.152
3.839-4.289	0.211	37	0.147	707	0.15	744	0.955	0.972	100	0.145
4.289-4.945	0.178	24	0.136	652	0.137	676	0.969	0.979	100	0.135
4.945-6.04	0.3	24	0.187	551	0.191	576	0.956	0.967	99.8264	0.186
6.04-8.471	0.196	18	0.189	442	0.19	460	0.96	0.963	100	0.19
8.471-46.72	0.167	16	0.183	271	0.182	289	0.971	0.966	99.308	0.193

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