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- PDB-1jf8: X-ray structure of reduced C10S, C15A arsenate reductase from pI258 -

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Basic information

Entry
Database: PDB / ID: 1jf8
TitleX-ray structure of reduced C10S, C15A arsenate reductase from pI258
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / PTPase I fold / P-loop / sulfinic acid
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
BICARBONATE ION / : / Arsenate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 20, 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.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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)15,0064
Polymers14,7841
Non-polymers2223
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.9, 34.2, 99.4
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: 14783.608 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: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A006
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg4000, Tris, potassium chloride, sodium arsenite, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
245 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→18 Å / Num. all: 44496 / Num. obs: 44496 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.7
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4254 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 299466
Reflection shell
*PLUS
% possible obs: 95.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of oxidised pI258 ArsC

Resolution: 1.12→18 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 4483 10 %random
Rwork0.2078 ---
all-44434 --
obs-44434 98 %-
Refinement stepCycle: LAST / Resolution: 1.12→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 13 220 1263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0108
X-RAY DIFFRACTIONc_angle_deg1.543
LS refinement shellResolution: 1.12→1.17 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.32 68 10.4 %
Rwork0.3306 --
obs-651 98 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 10.4 %

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