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- PDB-3rh0: Corynebacterium glutamicum mycothiol/mycoredoxin1-dependent arsen... -

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Basic information

Entry
Database: PDB / ID: 3rh0
TitleCorynebacterium glutamicum mycothiol/mycoredoxin1-dependent arsenate reductase Cg_ArsC2
ComponentsARSENATE REDUCTASE
KeywordsOXIDOREDUCTASE / Reductase
Function / homology
Function and homology information


arsenate-mycothiol transferase / mycothiol-arsenate ligase activity / response to arsenic-containing substance / cytoplasm
Similarity search - Function
Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arsenate-mycothiol transferase ArsC2 / Arsenate-mycothiol transferase ArsC2
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.724 Å
AuthorsMessens, J. / Wahni, K. / Dufe, T.V.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Corynebacterium glutamicum survives arsenic stress with arsenate reductases coupled to two distinct redox mechanisms
Authors: Villadangos, A.F. / Van Belle, K. / Wahni, K. / Dufe, T.V. / Freitas, S. / Nur, H. / De Galan, S. / Gil, J.A. / Collet, J.F. / Mateos, L.M. / Messens, J.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARSENATE REDUCTASE
B: ARSENATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)31,7272
Polymers31,7272
Non-polymers00
Water4,143230
1
A: ARSENATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)15,8641
Polymers15,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARSENATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)15,8641
Polymers15,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.350, 38.760, 43.860
Angle α, β, γ (deg.)100.60, 102.54, 99.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ARSENATE REDUCTASE / Protein-tyrosine-phosphatase


Mass: 15863.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: arsX, Cgl0263, cg0319 / Plasmid: pet28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NTP3, UniProt: P0DKS7*PLUS, arsenate reductase (glutathione/glutaredoxin)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 1.82 Å3/Da / Density % sol: 32.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2008
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.724→31.575 Å / Num. obs: 22115 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.15 Å2
Reflection shellResolution: 1.724→1.82 Å / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JE3

1je3


Resolution: 1.724→31.575 Å / SU ML: 0.21 / σ(F): 0.02 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1068 5.07 %Random
Rwork0.1766 ---
all0.269 22115 --
obs0.1796 21066 89.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.969 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 22.7023 Å2
Baniso -1Baniso -2Baniso -3
1-5.3677 Å2-11.5513 Å2-4.537 Å2
2--2.7884 Å26.7282 Å2
3----8.1561 Å2
Refinement stepCycle: LAST / Resolution: 1.724→31.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 230 2151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061957
X-RAY DIFFRACTIONf_angle_d1.0132648
X-RAY DIFFRACTIONf_dihedral_angle_d15.717746
X-RAY DIFFRACTIONf_chiral_restr0.065302
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.724-1.80250.34311120.23512077X-RAY DIFFRACTION74
1.8025-1.89750.29841320.21242345X-RAY DIFFRACTION84
1.8975-2.01640.29891220.18082478X-RAY DIFFRACTION88
2.0164-2.1720.21871460.16452541X-RAY DIFFRACTION91
2.172-2.39050.20751150.15892627X-RAY DIFFRACTION93
2.3905-2.73630.21141340.17252656X-RAY DIFFRACTION94
2.7363-3.44680.25071510.16192628X-RAY DIFFRACTION94
3.4468-31.58020.20621560.16532646X-RAY DIFFRACTION95
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)
10.2430.1835-0.20090.1382-0.0490.4407-0.03710.24070.0569-0.02180.11240.0469-0.1354-0.02910.01250.07740.01870.00920.0885-0.00750.1098-9.6053-8.854738.3747
20.04870.063-0.10430.1957-0.22390.3416-0.01130.05920.0178-0.0613-0.0156-0.0106-0.087-0.0033-0.00680.0793-0.01910.00240.1188-0.010.0965-8.566-9.151834.9924
30.11430.0516-0.09980.1788-0.1260.3870.0585-0.2122-0.10630.03130.0626-0.0372-0.14970.18310.00420.1377-0.03550.0050.14130.01520.1203-2.3569-9.100247.327
40.21110.09-0.05850.117-0.0890.29260.1435-0.172-0.14660.1462-0.1882-0.0746-0.05980.50610.01390.2076-0.119-0.06360.31470.09950.20583.0655-6.987750.331
50.07280.0692-0.04780.1119-0.08740.18090.205-0.0355-0.13860.0911-0.006-0.0690.329-0.1517-0.02310.1864-0.0629-0.03160.18240.03850.1361-20.0705-19.150348.0088
60.2843-0.18040.06760.3135-0.27240.5938-0.0766-0.1593-0.0997-0.0580.21550.1273-0.0609-0.28710.07580.06360.04640.02770.1270.00360.1028-18.8227-9.29545.8744
70.0752-0.03310.0040.0493-0.01570.184-0.06430.0099-0.01130.03130.043-0.015-0.08210.01520.00140.0662-0.00430.00430.055-0.01210.0650.72961.717325.6363
80.2058-0.0219-0.06170.1662-0.13240.3841-0.0111-0.0067-0.03360.09930.09510.10140.1148-0.1273-0.00060.14430.001-0.0290.13340.02330.1282-2.00930.460428.9983
90.2092-0.04120.14310.2362-0.01550.31240.01220.00330.0040.1323-0.00190.04520.02050.01150.00220.10150.00010.00240.09750.01010.09212.27172.249628.4063
100.0402-0.0194-0.01530.0518-0.07310.17780.0503-0.04240.00260.04040.1212-0.10960.01420.10360.02140.259-0.00720.04370.1313-0.02940.17728.4668-8.039317.9854
110.1006-0.0037-0.08120.1212-0.12040.5227-0.01290.0385-0.0087-0.20950.0536-0.1079-0.15720.107400.1338-0.00620.01230.0989-0.00490.09054.16198.339619.5416
120.0664-0.0558-0.05210.0863-0.060.26620.15350.1134-0.0401-0.1668-0.04810.04110.0243-0.0959-0.01370.13690.0245-0.02180.10620.00770.1104-6.18726.802418.2729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:49)
2X-RAY DIFFRACTION2(chain A and resid 50:71)
3X-RAY DIFFRACTION3(chain A and resid 72:85)
4X-RAY DIFFRACTION4(chain A and resid 86:98)
5X-RAY DIFFRACTION5(chain A and resid 99:109)
6X-RAY DIFFRACTION6(chain A and resid 110:128)
7X-RAY DIFFRACTION7(chain C and resid 1:21)
8X-RAY DIFFRACTION8(chain C and resid 22:41)
9X-RAY DIFFRACTION9(chain C and resid 42:83)
10X-RAY DIFFRACTION10(chain C and resid 84:89)
11X-RAY DIFFRACTION11(chain C and resid 90:117)
12X-RAY DIFFRACTION12(chain C and resid 118:129)

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