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- PDB-6eu7: Structure of the arsenite-bound form of AioX from Rhizobium sp. s... -

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Basic information

Entry
Database: PDB / ID: 6eu7
TitleStructure of the arsenite-bound form of AioX from Rhizobium sp. str. NT-26
ComponentsPutative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
KeywordsSIGNALING PROTEIN / Periplasmic-binding protein / Arsenic / arsenite-binding / Rhizobium NT-26
Function / homologyABC transporter, phosphonate, periplasmic substrate-binding protein / Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
Function and homology information
Biological speciesRhizobium sp. NT-26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDjordjevic, S. / Badilla, C. / Cole, A. / Santini, J.
Funding support Chile, United Kingdom, 2items
OrganizationGrant numberCountry
CONICYT Chile
Biotechnology and Biological Sciences Research CouncilBB/N012674/1 United Kingdom
CitationJournal: Sci Rep / Year: 2018
Title: A new family of periplasmic-binding proteins that sense arsenic oxyanions.
Authors: Badilla, C. / Osborne, T.H. / Cole, A. / Watson, C. / Djordjevic, S. / Santini, J.M.
History
DepositionOct 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
B: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
C: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
D: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
E: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
F: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)187,5196
Polymers187,5196
Non-polymers00
Water362
1
A: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Theoretical massNumber of molelcules
Total (without water)31,2531
Polymers31,2531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.359, 116.917, 136.838
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA45 - 30324 - 282
21ARGARGLEULEUBB45 - 30324 - 282
12ARGARGGLYGLYAA45 - 30424 - 283
22ARGARGGLYGLYCC45 - 30424 - 283
13VALVALLEULEUAA48 - 30327 - 282
23VALVALLEULEUDD48 - 30327 - 282
14VALVALLEULEUAA48 - 30327 - 282
24VALVALLEULEUEE48 - 30327 - 282
15VALVALLEULEUAA48 - 30327 - 282
25VALVALLEULEUFF48 - 30327 - 282
16ARGARGLEULEUBB45 - 30324 - 282
26ARGARGLEULEUCC45 - 30324 - 282
17VALVALLEULEUBB48 - 30327 - 282
27VALVALLEULEUDD48 - 30327 - 282
18VALVALLEULEUBB48 - 30327 - 282
28VALVALLEULEUEE48 - 30327 - 282
19VALVALLEULEUBB48 - 30327 - 282
29VALVALLEULEUFF48 - 30327 - 282
110VALVALLEULEUCC48 - 30327 - 282
210VALVALLEULEUDD48 - 30327 - 282
111VALVALLEULEUCC48 - 30327 - 282
211VALVALLEULEUEE48 - 30327 - 282
112VALVALLEULEUCC48 - 30327 - 282
212VALVALLEULEUFF48 - 30327 - 282
113VALVALGLYGLYDD48 - 30427 - 283
213VALVALGLYGLYEE48 - 30427 - 283
114VALVALGLYGLYDD48 - 30427 - 283
214VALVALGLYGLYFF48 - 30427 - 283
115VALVALGLYGLYEE48 - 30427 - 283
215VALVALGLYGLYFF48 - 30427 - 283

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Mass: 31253.197 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: residue CZS is an arsenite-modified cysteine / Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aioX, NT26_p10026 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NML6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 25 % PEG 3350, 0.1 M Tris-HCl / PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 3→136.838 Å / Num. obs: 62521 / % possible obs: 97.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 3→3.07 Å / Rmerge(I) obs: 0.587 / CC1/2: 0.651

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESK

6esk


Resolution: 3→136.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.906 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21495 3194 5.1 %RANDOM
Rwork0.19222 ---
obs0.19344 59325 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.286 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.11 Å2
2--1.63 Å20 Å2
3----3.05 Å2
Refinement stepCycle: 1 / Resolution: 3→136.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12167 0 0 2 12169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.95616831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44851546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62923.163588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.804152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.21515114
X-RAY DIFFRACTIONr_chiral_restr0.1270.21885
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219490
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4516.0346202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.3259.0427742
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.126.116208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.04256.17953678
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6960.14
12B6960.14
21A7100.11
22C7100.11
31A6980.14
32D6980.14
41A6980.13
42E6980.13
51A6860.14
52F6860.14
61B6940.12
62C6940.12
71B7020.12
72D7020.12
81B6840.14
82E6840.14
91B6960.12
92F6960.12
101C6960.13
102D6960.13
111C6900.11
112E6900.11
121C6860.14
122F6860.14
131D7060.13
132E7060.13
141D7080.13
142F7080.13
151E7020.13
152F7020.13
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 257 -
Rwork0.316 4405 -
obs--98.9 %

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