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- PDB-1sd8: ARSENATE REDUCTASE R60K MUTANT FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1sd8
TitleARSENATE REDUCTASE R60K MUTANT FROM E. COLI
ComponentsArsenate reductase
KeywordsOXIDOREDUCTASE / ARSC / REDUCTASE / ARSENITE / ARSENATE
Function / homology
Function and homology information


arsenate reductase (glutathione/glutaredoxin) / arsenate reductase (glutaredoxin) activity / response to arsenic-containing substance
Similarity search - Function
Arsenate reductase / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Arsenate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.59 Å
AuthorsDeMel, S. / Edwards, B.F.
CitationJournal: Protein Sci. / Year: 2004
Title: Arginine 60 in the ArsC arsenate reductase of E. coli plasmid R773 determines the chemical nature of the bound As(III) product.
Authors: DeMel, S. / Shi, J. / Martin, P. / Rosen, B.P. / Edwards, B.F.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 22, 2013Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.7Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.8Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.9Apr 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)16,7749
Polymers15,8211
Non-polymers9538
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Arsenate reductase
hetero molecules

A: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54818
Polymers31,6422
Non-polymers1,90516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3670 Å2
ΔGint-273 kcal/mol
Surface area13930 Å2
MethodPISA
3
A: Arsenate reductase
hetero molecules

A: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54818
Polymers31,6422
Non-polymers1,90516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area3420 Å2
ΔGint-255 kcal/mol
Surface area13960 Å2
MethodPISA
4
A: Arsenate reductase
hetero molecules

A: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54818
Polymers31,6422
Non-polymers1,90516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area2850 Å2
ΔGint-242 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.600, 86.600, 116.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-401-

CS

21A-1233-

HOH

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Components

#1: Protein Arsenate reductase / Arsenical pump modifier


Mass: 15821.226 Da / Num. of mol.: 1 / Mutation: R60K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P08692, arsenate reductase (glutathione/glutaredoxin)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 50% saturated Cesium Sulfate, 100mM sodium acetate, 5mM DTT, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 24, 2001 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. all: 33927 / Num. obs: 32216 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 16.9 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 25.9
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.2343 / Mean I/σ(I) obs: 3.88 / Rsym value: 0.2343 / % possible all: 69.2

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Processing

Software
NameVersionClassification
SHELXL-97refinement
XTALVIEWXGEN SHELXrefinement
X-GENdata reduction
X-GENdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NATIVE STRUCTURE

Resolution: 1.59→20 Å / Num. parameters: 13148 / Num. restraintsaints: 15242 / Cross valid method: FREE R / σ(F): 0
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 1682 5.2 %RANDOM
Rwork0.1396 ---
all0.1396 32216 --
obs-32216 91.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 1111 / Occupancy sum non hydrogen: 1415.7
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 20 330 1433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0315
X-RAY DIFFRACTIONs_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.044
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.074

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