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- PDB-1lk0: Disulfide intermediate of C89L Arsenate reductase from pI258 -

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Basic information

Entry
Database: PDB / ID: 1lk0
TitleDisulfide intermediate of C89L Arsenate reductase from pI258
Componentsarsenate reductase
KeywordsOXIDOREDUCTASE / PTPase I fold / P-loop / disulfide cascade
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: 1.6 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 23, 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_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arsenate reductase
B: arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8336
Polymers29,6842
Non-polymers1494
Water7,710428
1
A: arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9163
Polymers14,8421
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9163
Polymers14,8421
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.71, 35.48, 62.98
Angle α, β, γ (deg.)90, 118.01, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein arsenate reductase / ARSENICAL PUMP MODIFIER


Mass: 14841.753 Da / Num. of mol.: 2 / Mutation: C89L
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, EC: 1.97.1.5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, Tris, KCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
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
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 31235 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.033
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.065 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 32094 / Num. measured all: 214661 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 97.6 % / Mean I/σ(I) obs: 14.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C10SC15A ArsC (PDB ENTRY 1JF8)

1jf8


Resolution: 1.6→27.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2341 1549 random
Rwork0.203 --
all0.21 31225 -
obs0.21 31225 -
Refinement stepCycle: LAST / Resolution: 1.6→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 4 428 2510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010695
X-RAY DIFFRACTIONc_angle_d1.512
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.51

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