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- PDB-1lju: X-RAY STRUCTURE OF C15A ARSENATE REDUCTASE FROM PI258 COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1lju
TitleX-RAY STRUCTURE OF C15A ARSENATE REDUCTASE FROM PI258 COMPLEXED WITH ARSENITE
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / PTPASE I FOLD / P-LOOP
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
: / Arsenate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZegers, I. / Martins, J.C. / Willem, R. / Wyns, L. / Messens, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade.
Authors: Messens, J. / Martins, J.C. / Van Belle, K. / Brosens, E. / Desmyter, A. / De Gieter, M. / Wieruszeski, J.M. / Willem, R. / Wyns, L. / Zegers, I.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: 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)14,9632
Polymers14,9241
Non-polymers391
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.97, 37.83, 106.37
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: 14923.601 Da / Num. of mol.: 1 / Mutation: C15A
Source method: isolated from a genetically manipulated source
Details: oxidised / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: arsc / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A006, EC: 1.97.1.5
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: PEG4000, TRIS, KCl, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl11pH8.0
2100 mM11KCl
310 mMarsenite12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.4→25 Å / Num. all: 27869 / Num. obs: 26420 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 0.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 34
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 2732 / Rsym value: 0.239 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 27888 / Num. measured all: 188689 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.77

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF OXIDISED PI258 ARSC (PDB ENTRY 1JFV)

1jfv


Resolution: 1.4→20.94 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1274 10 %RANDOM
Rwork0.2414 ---
all0.26 26371 --
obs0.26 26371 --
Refinement stepCycle: LAST / Resolution: 1.4→20.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 1 229 1272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.4→1.46 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.32 68 10.4 %
Rwork0.3306 --
obs--98 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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