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- PDB-8p6m: Arsenate reductase (ArsC2) from Deinococcus indicus -

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Basic information

Entry
Database: PDB / ID: 8p6m
TitleArsenate reductase (ArsC2) from Deinococcus indicus
ComponentsLow molecular weight phosphatase family protein
KeywordsOXIDOREDUCTASE / bioremediation / arsenic / LMW-PTPase / reductase / METAL BINDING PROTEIN
Function / homologyPhosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / response to arsenic-containing substance / Low molecular weight phosphatase family protein
Function and homology information
Biological speciesDeinococcus indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGouveia, A.G. / Matias, P.M. / Romao, C.V.
Funding support Portugal, 4items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/31317/2017 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0087/2020 Portugal
CitationJournal: Front Microbiol / Year: 2023
Title: Unraveling the multifaceted resilience of arsenic resistant bacterium Deinococcus indicus .
Authors: Gouveia, A.G. / Salgueiro, B.A. / Ranmar, D.O. / Antunes, W.D.T. / Kirchweger, P. / Golani, O. / Wolf, S.G. / Elbaum, M. / Matias, P.M. / Romao, C.V.
History
DepositionMay 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low molecular weight phosphatase family protein
B: Low molecular weight phosphatase family protein


Theoretical massNumber of molelcules
Total (without water)31,5222
Polymers31,5222
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint0 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.673, 39.401, 72.385
Angle α, β, γ (deg.)90.000, 97.383, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Low molecular weight phosphatase family protein


Mass: 15760.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Arsenic resistant / Source: (gene. exp.) Deinococcus indicus (bacteria) / Strain: Wt/1a / Gene: CBQ26_01585 / Plasmid: pET28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A246BSD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium Acetate trihdrate, 0.1M Tris-HCl, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→19.7 Å / Num. obs: 25923 / % possible obs: 87.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 29.476 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.077 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique obs: 994 / CC1/2: 0.485 / Rpim(I) all: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.7 Å / SU ML: 0.2217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 1272 4.91 %
Rwork0.2235 24627 -
obs0.225 25899 87.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 262 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472065
X-RAY DIFFRACTIONf_angle_d0.67392821
X-RAY DIFFRACTIONf_chiral_restr0.0436322
X-RAY DIFFRACTIONf_plane_restr0.0053369
X-RAY DIFFRACTIONf_dihedral_angle_d12.3001731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.34531100.25922087X-RAY DIFFRACTION67.43
1.72-1.790.26981190.26072365X-RAY DIFFRACTION76.17
1.79-1.890.31911270.26122589X-RAY DIFFRACTION82.58
1.89-2.010.27911480.24692799X-RAY DIFFRACTION89.85
2.01-2.160.27341410.22362988X-RAY DIFFRACTION95.4
2.16-2.380.26421590.20922978X-RAY DIFFRACTION95.87
2.38-2.720.25661620.21393016X-RAY DIFFRACTION95.81
2.72-3.430.22451410.21042949X-RAY DIFFRACTION92.9
3.43-19.70.2341650.22282856X-RAY DIFFRACTION88.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.10132636064-0.02453435508890.28141762982.04749708495-0.01680179999561.53420364242-0.00130469764375-0.146970664854-0.0592162948459-0.0726190274650.05760163341270.237751486099-0.078143275532-0.163343245417-0.03865918323660.1083863704120.0236350095013-0.007475213186910.09402783766890.01255028457180.128431092567-7.60271666878-5.1412811197-32.0374921537
26.223639516042.00520403344.741115403450.7113358197531.783461764154.587787914550.346730442992-0.893512698296-0.1032863415330.311234725601-0.1655499613910.2838915402620.383864140989-0.511789240231-0.167867066840.206022567129-0.01867017166740.01506893989150.1925762980050.02497835638460.318292219543-12.4132509998-16.3247593052-32.2263312767
33.266709594840.5095893622791.401553043242.539963583441.024699489775.842090234280.0261417839206-0.0922455870161-0.03950044811890.1238630567250.0231321595979-0.002337825172590.224880189940.239911336015-0.04938750764190.1038873936870.02229662298450.03013456215130.07084651021440.00813919906030.07493868888322.85851260935-12.591735392-30.3379509724
43.46530407794-0.394479849086-0.5696161142041.758261465970.141821368171.36979549322-0.03153274234150.101458862101-0.007189631934770.009237719079360.05508701270250.2696951140610.073866521023-0.137279523241-0.01278071715670.102994428301-0.0304290696943-0.0001909456726840.0866932354240.02947499818730.113271817051-12.6305392181.50831448958-3.57717595013
57.186502025550.0638255323407-1.288570092712.29784868642.780661408663.622590782350.2914051948921.078183831460.461991179285-0.415556000728-0.07502749677880.61123703907-0.891859451584-0.885294643738-0.2869929250060.2834697362610.09858260056050.01931969630220.3075616453990.1009433851480.490812538665-22.578747868910.3354481521-5.43486122178
62.43218420126-0.417495068307-1.073615038671.815785395671.143146464161.332163809370.1040839889880.1489133850220.191468351864-0.1583954499150.0250028777113-0.109759542102-0.136214451776-0.00869936035213-0.1097774281210.13449658708-0.006720105776080.004427449382130.1003445503080.03171351668450.0768858768049-4.594585642229.80761070496-5.90782770544
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 81 )AA8 - 811 - 74
22chain 'A' and (resid 82 through 110 )AA82 - 11075 - 95
33chain 'A' and (resid 111 through 144 )AA111 - 14496 - 129
44chain 'B' and (resid 8 through 85 )BB8 - 851 - 78
55chain 'B' and (resid 86 through 101 )BB86 - 10179 - 89
66chain 'B' and (resid 102 through 143 )BB102 - 14390 - 131

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