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- PDB-6xl2: Structure of the arsenate-bound form of ArrX from Chrysiogenes ar... -

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Basic information

Entry
Database: PDB / ID: 6xl2
TitleStructure of the arsenate-bound form of ArrX from Chrysiogenes arsenatis
ComponentsArrX
KeywordsSIGNALING PROTEIN / Periplasmic binding protein
Function / homologyARSENATE
Function and homology information
Biological speciesChrysiogenes arsenatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMaher, M.J. / Poddar, N.
CitationJournal: 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
DepositionJun 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArrX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4782
Polymers34,3391
Non-polymers1391
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area12230 Å2
Unit cell
Length a, b, c (Å)52.811, 53.453, 90.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AsO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 293 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 Soaked in:5 mM Na2HAsO4, 0.1 M Tris pH 8.5, 27% (w/v) PEG 3350, 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.74→46.04 Å / Num. obs: 27069 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 1435 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X6B

6x6b


Resolution: 1.74→46.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.642 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1371 5.1 %RANDOM
Rwork0.1881 ---
obs0.1902 25646 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.71 Å2 / Biso mean: 24.719 Å2 / Biso min: 14.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2--0.92 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.74→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 5 156 2193
Biso mean--38.49 33.54 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172050
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.6483017
X-RAY DIFFRACTIONr_angle_other_deg1.2551.5664761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83320.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3451520
X-RAY DIFFRACTIONr_chiral_restr0.060.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
LS refinement shellResolution: 1.74→1.784 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 84 -
Rwork0.263 1874 -
obs--98.74 %

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