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- PDB-1jfv: X-Ray Structure of oxidised C10S, C15A arsenate reductase from pI258 -

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Basic information

Entry
Database: PDB / ID: 1jfv
TitleX-Ray Structure of oxidised C10S, C15A arsenate reductase from pI258
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / oxidised / arsenate reductase / perchlorate / potassium
Function / homology
Function and homology information


arsenate reductase (thioredoxin) / arsenate reductase (thioredoxin) activity / response to arsenic-containing substance / protein tyrosine phosphatase activity / metal ion binding / cytoplasm
Similarity search - Function
Arsenate reductase ArsC / 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
: / PERCHLORATE ION / Arsenate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZegers, I. / Martins, J.C. / Willem, R. / Wyns, L. / Messens, J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Arsenate reductase from S. aureus plasmid pI258 is a phosphatase drafted for redox duty.
Authors: Zegers, I. / Martins, J.C. / Willem, R. / Wyns, L. / Messens, J.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0163
Polymers14,8771
Non-polymers1392
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.8, 35.63, 109.53
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein arsenate reductase / ARSENICAL PUMP MODIFIER


Mass: 14877.399 Da / Num. of mol.: 1 / Mutation: C10S,C15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: arsC / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P0A006
#2: Chemical ChemComp-LCP / PERCHLORATE ION


Mass: 99.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg4000, arsenite, sodium perchlorate, potassium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1reservoir
2100 mM1reservoirNaClO4
342.5 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.043, 1.0425, 0.9918
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 1, 2000
RadiationMonochromator: double crystal focussing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0431
21.04251
30.99181
ReflectionResolution: 2→30 Å / Num. all: 9502 / Num. obs: 9502 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 34 % / Biso Wilson estimate: 21.05 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 47
Reflection shellResolution: 2→2.07 Å / Redundancy: 30 % / Rmerge(I) obs: 0.361 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 162849 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 7.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→17 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 503 5.3 %random
Rwork0.2364 ---
all-9448 --
obs-9448 --
Refinement stepCycle: LAST / Resolution: 2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 6 125 1162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.3344 48 -
Rwork0.3293 --
obs-872 100 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.86

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