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- PDB-1ljl: Wild Type pI258 S. aureus arsenate reductase -

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Basic information

Entry
Database: PDB / ID: 1ljl
TitleWild Type pI258 S. aureus arsenate reductase
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / 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: 2.01 Å
AuthorsMessens, J. / Martins, J.C. / Van Belle, K. / Brosens, E. / Desmyter, A. / De Gieter, M. / Wieruszeski, J.M. / Willem, R. / Wyns, L. / Zegers, I.
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 21, 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8712
Polymers14,8321
Non-polymers391
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.450, 32.770, 100.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein arsenate reductase / ARSENICAL PUMP MODIFIER


Mass: 14831.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: reduced / 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.: 100 / 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: 1.81 Å3/Da / Density % sol: 31.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 393K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
2100 mM1dropKCl
3100 mMTris-HCl1reservoirpH8.0
450 mMammonium bicarbonate1reservoir
542.5 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 15, 2002
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 7503 / Num. obs: 7503 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.05 / Num. unique all: 751 / Rsym value: 0.43 / % possible all: 74.8
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 96.5 % / Num. measured all: 203478 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 74.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JF8

1jf8


Resolution: 2.01→14.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 564 -random
Rwork0.214 ---
all0.23 7466 --
obs0.23 7466 96 %-
Refinement stepCycle: LAST / Resolution: 2.01→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 1 100 1132
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Rfactor all: 0.23 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.55

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