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- PDB-3t38: Corynebacterium glutamicum thioredoxin-dependent arsenate reducta... -

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Basic information

Entry
Database: PDB / ID: 3t38
TitleCorynebacterium glutamicum thioredoxin-dependent arsenate reductase Cg_ArsC1'
ComponentsArsenate Reductase
KeywordsOXIDOREDUCTASE / Low molecular weight tyrosine phosphatase fold / Reduction of arsenate to arsenite
Function / homology
Function and homology information


Oxidoreductases / response to arsenic-containing substance / oxidoreductase activity
Similarity search - Function
Corynebacterium glutamicum thioredoxin-dependent arsenate reductase, N-terminal domain / : / Protein-tyrosine-phosphatase-like, N-terminal domain / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Helicase, Ruva Protein; domain 3 / Rossmann fold ...Corynebacterium glutamicum thioredoxin-dependent arsenate reductase, N-terminal domain / : / Protein-tyrosine-phosphatase-like, N-terminal domain / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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. / Tamu Dufe, V. / Freitas, S. / Nur, H. / De Galan, S. / Gil, J.A. / Collet, J.F. / Mateos, L.M. / Messens, J.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Structure summary
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1513
Polymers46,9982
Non-polymers1521
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.800, 75.500, 58.100
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arsenate Reductase / Protein-tyrosine-phosphatase / Arsenate Reductase


Mass: 23499.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: arsc1 prime, cg1707, Cgl1512 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8NQC6, Oxidoreductases
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG4000, 0.1M Tris, 0.1M NaClO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 77.36 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→24.37 Å / Num. obs: 35383 / % possible obs: 75 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 2.2 Å / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→24.38 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.968 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23103 899 5 %RANDOM
Rwork0.17708 ---
obs0.17987 17089 100 %-
all-35383 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.39 Å2
2--0.27 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 8 69 3100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223091
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9644196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1423.684133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54815516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2841520
X-RAY DIFFRACTIONr_chiral_restr0.130.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212298
X-RAY DIFFRACTIONr_mcbond_it0.8911.51935
X-RAY DIFFRACTIONr_mcangle_it1.63123122
X-RAY DIFFRACTIONr_scbond_it2.96231156
X-RAY DIFFRACTIONr_scangle_it4.3954.51074
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 66 -
Rwork0.266 1251 -
obs--100 %
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)
16.23821.4631-5.17834.93620.365611.2438-0.43910.1043-0.43660.12290.2811-0.13960.85720.51860.15810.20360.0641-0.0140.0634-0.04420.267835.518513.559723.7509
22.2068-0.2033-0.73971.49840.3154.2412-0.08140.0856-0.21960.0469-0.0362-0.07750.34010.30880.11760.10130.01440.01170.0346-0.00610.115331.956423.161330.4222
31.7521.44420.79561.73880.29144.6747-0.0084-0.1836-0.08950.0924-0.0766-0.0461-0.02190.12280.0850.09660.03310.01840.0557-0.00470.129532.253932.780640.8601
42.84111.2664-2.08576.8185-5.43445.44140.1819-0.43450.46030.7546-0.237-0.1085-0.70770.0120.05510.30090.0011-0.01790.2899-0.08130.235832.550539.64850.6417
52.11610.73830.32754.53260.84595.0534-0.0813-0.1628-0.07050.0125-0.07240.45050.2242-0.86450.15370.0154-0.04320.0080.2676-0.02930.162615.016124.191724.4904
62.07890.29471.25222.02970.04294.8989-0.14710.18770.2231-0.1142-0.12830.2496-0.4887-0.56080.27540.17750.0389-0.03710.1491-0.0060.162319.514235.361710.0932
73.6734-1.9168-1.01776.20420.62747.1498-0.1626-0.03890.54-0.0459-0.0181-0.7552-0.33070.52030.18070.1765-0.0888-0.04840.2780.05670.244132.673532.86528.3908
87.7222-1.626-2.377515.95077.098212.7581-0.26630.63430.6713-0.41720.23-0.3546-1.2329-0.43130.03640.35190.0975-0.04940.21850.10330.112322.728138.8403-2.5515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 29
2X-RAY DIFFRACTION2A30 - 89
3X-RAY DIFFRACTION3A90 - 176
4X-RAY DIFFRACTION4A177 - 212
5X-RAY DIFFRACTION5B9 - 74
6X-RAY DIFFRACTION6B75 - 159
7X-RAY DIFFRACTION7B160 - 192
8X-RAY DIFFRACTION8B193 - 212

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