PDB-6x9g: Structure of the malonate-bound form of ArrX from Chrysiogenes ar...

ID or keywords:

Entry

Database: PDB / ID: 6x9g

Title

Structure of the malonate-bound form of ArrX from Chrysiogenes arsenatis

Components

ArrX

Keywords

SIGNALING PROTEIN / Periplasmic binding protein

Function / homology

MALONATE ION

Function and homology information

Biological species

Chrysiogenes arsenatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 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	Jun 2, 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	6x9g.cif.gz	74.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6x9g.ent.gz	51.6 KB	Display	PDB format
PDBx/mmJSON format	6x9g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6x9g_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	6x9g_full_validation.pdf.gz	443.7 KB	Display
Data in XML	6x9g_validation.xml.gz	14 KB	Display
Data in CIF	6x9g_validation.cif.gz	20 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x9/6x9g ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x9g	HTTPS FTP

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Related structure data

Related structure data	6x6bSC 6x8wC 6xabC 6xadC 6xl2C 7l22C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7l22-d 6x6b-d 6x8w-d 5lq1-1 5aaf-d 5ayg-1 3d15-d 4ueu-d 6eu7-1 4zjr-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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)	52.406, 55.602, 91.440
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-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1 M sodium malonate pH 6.7, 18% (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: Mar 2, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 1.68→47.51 Å / Num. obs: 31216 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC_1/2: 0.999 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.68→1.71 Å / Num. unique obs: 1496 / CC_1/2: 0.9

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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: 1.68→47.508 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.949 / SU B: 1.953 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2007	1529	4.907 %
R_work	0.1704	29630	-
all	0.172	-	-
obs	-	29630	99.734 %

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: 21.632 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.178 Å²	0 Å²	0 Å²
2-	-	1.624 Å²	0 Å²
3-	-	-	-0.446 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→47.508 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2030	0	7	207	2244

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	2182
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2035
X-RAY DIFFRACTION	r_angle_refined_deg	1.27	1.647	2986
X-RAY DIFFRACTION	r_angle_other_deg	1.302	1.566	4722
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.806	5	289
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.01	20.787	127
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.112	15	368
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.681	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	285
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2499
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	500
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	411
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.171	0.2	1927
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1056
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	894
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.257	0.2	170
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.02	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	1.064	2.091	1057
X-RAY DIFFRACTION	r_mcbond_other	1.061	2.088	1056
X-RAY DIFFRACTION	r_mcangle_it	1.745	3.129	1328
X-RAY DIFFRACTION	r_mcangle_other	1.745	3.132	1329
X-RAY DIFFRACTION	r_scbond_it	1.77	2.355	1125
X-RAY DIFFRACTION	r_scbond_other	1.769	2.353	1122
X-RAY DIFFRACTION	r_scangle_it	2.816	3.443	1641
X-RAY DIFFRACTION	r_scangle_other	2.815	3.444	1642
X-RAY DIFFRACTION	r_lrange_it	5.148	40.428	9215
X-RAY DIFFRACTION	r_lrange_other	4.839	39.98	9042

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
1.679-1.722	0.267	112	0.236	2092	0.237	2265	0.864	0.876	97.3068	0.219
1.722-1.769	0.212	108	0.206	2100	0.206	2209	0.909	0.918	99.9547	0.187
1.769-1.821	0.218	94	0.193	2070	0.194	2165	0.936	0.926	99.9538	0.175
1.821-1.877	0.191	105	0.181	1998	0.182	2103	0.93	0.942	100	0.162
1.877-1.938	0.231	109	0.176	1917	0.178	2027	0.927	0.95	99.9507	0.157
1.938-2.006	0.209	90	0.175	1875	0.176	1965	0.942	0.949	100	0.157
2.006-2.082	0.216	83	0.17	1818	0.172	1901	0.938	0.95	100	0.155
2.082-2.166	0.203	99	0.163	1736	0.165	1835	0.953	0.96	100	0.146
2.166-2.262	0.213	100	0.173	1656	0.175	1757	0.937	0.954	99.9431	0.153
2.262-2.373	0.169	94	0.163	1604	0.163	1698	0.964	0.965	100	0.148
2.373-2.501	0.156	88	0.169	1532	0.168	1621	0.968	0.963	99.9383	0.155
2.501-2.652	0.241	78	0.169	1442	0.173	1522	0.933	0.951	99.8686	0.157
2.652-2.834	0.178	62	0.17	1380	0.171	1445	0.961	0.961	99.7924	0.161
2.834-3.06	0.182	75	0.16	1278	0.162	1353	0.962	0.965	100	0.157
3.06-3.351	0.199	54	0.171	1176	0.172	1231	0.954	0.961	99.9188	0.171
3.351-3.744	0.192	41	0.16	1109	0.161	1150	0.962	0.968	100	0.164
3.744-4.319	0.159	40	0.154	968	0.154	1008	0.974	0.973	100	0.163
4.319-5.279	0.186	42	0.147	820	0.149	865	0.972	0.975	99.6532	0.159
5.279-7.42	0.241	33	0.204	657	0.206	694	0.949	0.965	99.4236	0.214
7.42-47.508	0.32	22	0.185	401	0.192	427	0.942	0.961	99.0632	0.213

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