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- PDB-8p5n: Arsenate reductase (ArsC2) from Deinococcus indicus, co-crystalli... -

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Basic information

Entry
Database: PDB / ID: 8p5n
TitleArsenate reductase (ArsC2) from Deinococcus indicus, co-crystallized with arsenate
ComponentsLow molecular weight phosphatase family protein
KeywordsOXIDOREDUCTASE / bioremediation / arsenic / LMW-PTPase / reductase
Function / homologyPhosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / ARSENATE / Low molecular weight phosphatase family protein
Function and homology information
Biological speciesDeinococcus indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9846
Polymers31,5222
Non-polymers4624
Water5,477304
1
A: Low molecular weight phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9923
Polymers15,7611
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Low molecular weight phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9923
Polymers15,7611
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.513, 39.822, 72.194
Angle α, β, γ (deg.)90.000, 97.075, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 35 or resid 37...
d_2ens_1(chain "B" and (resid 8 through 35 or resid 37...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROGLYGLYAA8 - 358 - 35
d_12TYRTYRLEULEUAA37 - 6737 - 67
d_13ALAALAALAALAAA69 - 13469 - 134
d_14ILEILEALAALAAA136 - 142136 - 142
d_15ARTARTARTARTAC201
d_16GOLGOLGOLGOLAD202
d_21PROPROGLYGLYBB8 - 358 - 35
d_22TYRTYRLEULEUBB37 - 6737 - 67
d_23ALAALAALAALABB69 - 13469 - 134
d_24ILEILEALAALABB136 - 142136 - 142
d_25ARTARTARTARTBE201
d_26GOLGOLGOLGOLBF202

NCS oper: (Code: givenMatrix: (0.999988084451, 0.00090828120668, 0.00479645507371), (0.000718659970787, -0.999223717224, 0.0393884052205), (0.00482850741647, -0.0393844888657, -0.99921246367)Vector: ...NCS oper: (Code: given
Matrix: (0.999988084451, 0.00090828120668, 0.00479645507371), (0.000718659970787, -0.999223717224, 0.0393884052205), (0.00482850741647, -0.0393844888657, -0.99921246367)
Vector: 4.60529344856, 34.8086270291, -35.1936954646)

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Components

#1: Protein Low molecular weight phosphatase family protein / Arsenate reductase (ArsC2)


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: Chemical ChemComp-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AsO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30 % (w/v) PEG 4000, 0.1 M Dibasic Heptahydratesodium Arsenate.

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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: 1.5→19.91 Å / Num. obs: 35509 / % possible obs: 89.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Net I/σ(I): 10.6
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1775 / CC1/2: 0.725 / Rpim(I) all: 0.347 / Rrim(I) all: 0.62 / % possible all: 41.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.91 Å / SU ML: 0.1246 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.1334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1716 1730 4.87 %
Rwork0.1525 33776 -
obs0.1534 35506 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.75 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 20 307 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362200
X-RAY DIFFRACTIONf_angle_d0.66983002
X-RAY DIFFRACTIONf_chiral_restr0.0587336
X-RAY DIFFRACTIONf_plane_restr0.006397
X-RAY DIFFRACTIONf_dihedral_angle_d12.2695789
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.54259887781 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.267560.21661132X-RAY DIFFRACTION36.5
1.54-1.590.2386930.2122139X-RAY DIFFRACTION67.74
1.59-1.650.22711440.20752823X-RAY DIFFRACTION90.57
1.65-1.720.21271710.18683016X-RAY DIFFRACTION97.73
1.72-1.790.22121660.17353039X-RAY DIFFRACTION97.65
1.79-1.890.16851430.15623085X-RAY DIFFRACTION97.82
1.89-2.010.19591550.15113044X-RAY DIFFRACTION98.16
2.01-2.160.16311510.13743097X-RAY DIFFRACTION98.13
2.16-2.380.15091470.13513066X-RAY DIFFRACTION97.87
2.38-2.720.15291450.14523121X-RAY DIFFRACTION98.31
2.72-3.430.18781720.14523102X-RAY DIFFRACTION97.91
3.43-19.910.14581870.14813112X-RAY DIFFRACTION96.69
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)
12.85101398648-0.380819622551-0.4057296942242.45060377317-0.5997028958082.037729506790.013486149606-0.1747473250010.01267832566070.2145469624210.0405873189361-0.196922209719-0.1263192503170.226507328141-0.06746879714040.093792983383-0.01236166512880.000326608323360.0898949961243-0.01457233218540.126590314365-5.450403596911.6231378696-0.723932519409
23.698689894460.1662105150320.1619109251582.89951244853-0.0198725218460.2525681459730.0619380525297-0.2078644418520.07907136587580.1231402933590.0371936240399-0.0155678354565-0.124412036450.0738362531348-0.0819439717640.0702830483536-0.001760010148690.003742837120790.0723253305141-0.008683336331340.0684891449058-11.342882301612.80740348921.41719295997
33.03267894944-0.289284386522-0.2540069355741.33805947040.01462765176891.211647056010.02216224874340.181790178670.157403504347-0.121693934463-0.0101863314843-0.142875419127-0.0596062885332-0.00717443876387-0.02908849193410.108841938691-0.0104717127940.01347085693970.0719698286271-0.002257169031950.105407679432-14.316933285517.7521296083-8.3343374289
46.088763935261.44002641136-0.9821677394594.0853526909-4.534584673375.09717829585-0.0157278753270.08202162119650.123363878687-0.143806356745-0.287689497192-0.4710340015780.09453658492850.1774880497190.3252320584160.1342441658870.004094508103530.004393176878980.118375137435-0.02266804695070.1672322793324.2733969809812.8756506689-2.60338486172
53.140747741670.1241985365821.133498141121.17999407782-0.2516120608742.18415753570.05536112862850.226405578174-0.313553345332-0.2366210597880.00704804148152-0.1260321279510.1749601284750.157470091773-0.08248840980150.1432442285380.02529984763010.003224000094110.0964828024558-0.01436537488560.147457550452-4.387295836832.94900739785-5.91945401806
62.07978353946-0.1192065081220.676786314031.59592682937-1.036189397094.781130895590.01743042038260.0254042021948-0.0108263677664-0.09873122889090.02103848343850.03429554757910.110818454788-0.179071939878-0.07084417356530.0817892829669-0.01263336671370.004533431967090.0657028403028-0.006983755284790.0828891120013-20.00620670126.55905394388-5.67733091677
72.557359430370.177556778269-0.365582229951.85155028713-0.3109972824371.18255953977-0.001625969136120.0237533543279-0.0741066700163-0.03113942936860.0269685147352-0.1991638200130.089419043880.07753289974-0.02703158715710.1201617406070.0229652314105-0.006100869183380.1169328317-0.02283114518310.134165026143-7.138288709820.1015578575-32.2178881991
83.81237790343-1.438146364511.986406914525.38333136195-4.13500605133.433308972330.0248840109443-0.102585951475-0.1462471697070.1609029444410.154024157462-0.0812052784143-0.1359538635320.0557299170359-0.1554331981390.1516909389640.03325684053190.03276579890070.189214052289-0.02670483623820.3759234759298.6215340405422.0255887592-33.1807984742
93.25285293913-0.364787480564-1.399051059181.520027172130.5593011111925.372382270640.0303151385263-0.4814320197690.462974612930.326649736426-0.0674938921489-0.475171912838-0.392375917690.303038352983-0.08416805903760.208542873172-0.0260299232822-0.03802517374990.183163857405-0.04929406649580.2811788075851.9411905552830.5654674306-27.8221967448
102.158173867210.336173679511-1.220858433421.82478047309-0.8576003209382.150685801350.0560602176052-0.0994286683690.1431075044320.1594425625590.0407985268815-0.00864206603105-0.1376160297830.0184642602866-0.09849528087490.1398458848790.0161846193243-0.002589902403910.122556291114-0.01094124798990.118037828428-12.506541046329.0220487543-29.6229775806
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 20 )AA6 - 201 - 15
22chain 'A' and (resid 21 through 43 )AA21 - 4316 - 38
33chain 'A' and (resid 44 through 72 )AA44 - 7239 - 67
44chain 'A' and (resid 73 through 81 )AA73 - 8168 - 76
55chain 'A' and (resid 82 through 110 )AA82 - 11077 - 105
66chain 'A' and (resid 111 through 143 )AA111 - 143106 - 138
77chain 'B' and (resid 8 through 72 )BD8 - 721 - 65
88chain 'B' and (resid 73 through 81 )BD73 - 8166 - 74
99chain 'B' and (resid 82 through 100 )BD82 - 10075 - 93
1010chain 'B' and (resid 101 through 142 )BD101 - 14294 - 135

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