PDB-6x6b: Structure of the sulfate-bound form of ArrX from Chrysiogenes ars...

ID or keywords:

Entry

Database: PDB / ID: 6x6b

Title

Structure of the sulfate-bound 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: 1.67 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	May 27, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 24, 2021	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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Download

PDBx/mmCIF format	6x6b.cif.gz	74 KB	Display	PDBx/mmCIF format
PDB format	pdb6x6b.ent.gz	50.6 KB	Display	PDB format
PDBx/mmJSON format	6x6b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6b ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6b	HTTPS FTP

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Related structure data

Related structure data	6x8wC 6x9gC 6xabC 6xadC 6xl2C 7l22C 6eskS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6x8w-d 7l22-d 6x9g-d 4gvo-1 3daj-d 4foo-1 6nq4-1 2xng-d 5aaf-d 3miy-1 Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ArrX

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.800, 53.200, 89.840
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.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.84 Å³/Da / Density % sol: 33.05 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.67→45.7 Å / Num. obs: 29902 / % possible obs: 99.4 % / Redundancy: 12.9 % / CC_1/2: 0.997 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.67→1.71 Å / Num. unique obs: 2161 / CC_1/2: 0.524

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ESK

6esk

Resolution: 1.67→45.7 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.951 / SU B: 2.582 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2043	1447	4.8 %
R_work	0.1747	28407	-
all	0.176	-	-
obs	-	28407	99.275 %

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: 30.458 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.126 Å²	0 Å²	0 Å²
2-	-	0.817 Å²	0 Å²
3-	-	-	0.309 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→45.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2020	0	28	182	2230

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	2131
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1991
X-RAY DIFFRACTION	r_angle_refined_deg	1.366	1.643	2902
X-RAY DIFFRACTION	r_angle_other_deg	1.312	1.565	4609
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.938	5	271
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.402	20.769	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.647	15	354
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.272	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	277
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2388
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	477
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	409
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	1880
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1042
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1003
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.202	0.2	158
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.072	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.178	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.448	0.2	24
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.074	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.582	2.983	1037
X-RAY DIFFRACTION	r_mcbond_other	1.582	2.981	1036
X-RAY DIFFRACTION	r_mcangle_it	2.282	4.47	1299
X-RAY DIFFRACTION	r_mcangle_other	2.281	4.473	1300
X-RAY DIFFRACTION	r_scbond_it	2.603	3.359	1094
X-RAY DIFFRACTION	r_scbond_other	2.601	3.361	1095
X-RAY DIFFRACTION	r_scangle_it	3.915	4.904	1594
X-RAY DIFFRACTION	r_scangle_other	3.914	4.906	1595
X-RAY DIFFRACTION	r_lrange_it	5.156	36.579	2413
X-RAY DIFFRACTION	r_lrange_other	5.155	36.591	2414

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
1.67-1.713	0.278	116	0.272	2040	0.273	2196	0.766	0.76	98.1785	0.264
1.713-1.76	0.299	117	0.252	1952	0.255	2104	0.777	0.815	98.3365	0.242
1.76-1.811	0.264	93	0.251	1956	0.252	2065	0.844	0.854	99.2252	0.235
1.811-1.867	0.248	94	0.226	1914	0.227	2028	0.883	0.892	99.0138	0.208
1.867-1.928	0.29	85	0.215	1856	0.218	1963	0.88	0.904	98.8793	0.194
1.928-1.995	0.212	108	0.191	1757	0.192	1884	0.923	0.93	98.9915	0.171
1.995-2.071	0.216	78	0.184	1745	0.185	1841	0.917	0.935	99.0223	0.166
2.071-2.155	0.211	95	0.174	1661	0.176	1769	0.935	0.942	99.2651	0.155
2.155-2.251	0.198	94	0.168	1586	0.169	1689	0.949	0.954	99.4671	0.15
2.251-2.36	0.19	78	0.152	1540	0.153	1627	0.949	0.962	99.4468	0.134
2.36-2.488	0.198	61	0.144	1490	0.146	1559	0.949	0.965	99.4869	0.128
2.488-2.638	0.19	58	0.147	1412	0.148	1473	0.958	0.965	99.7963	0.131
2.638-2.819	0.206	69	0.16	1322	0.162	1392	0.952	0.961	99.9282	0.142
2.819-3.044	0.176	51	0.159	1233	0.159	1284	0.958	0.964	100	0.143
3.044-3.333	0.163	69	0.166	1140	0.166	1209	0.964	0.962	100	0.15
3.333-3.724	0.176	42	0.149	1058	0.15	1100	0.967	0.971	100	0.138
3.724-4.296	0.162	48	0.145	917	0.145	966	0.957	0.966	99.8965	0.137
4.296-5.25	0.177	42	0.17	808	0.17	850	0.792	0.758	100	0.163
5.25-7.376	0.276	36	0.228	628	0.231	665	0.234	0.297	99.8496	0.219
7.376-45.776	0.276	13	0.189	392	0.192	408	0.704	0.813	99.2647	0.185

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