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- PDB-1jzw: Arsenate Reductase + Sodium Arsenate From E. coli -

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Basic information

Entry
Database: PDB / ID: 1jzw
TitleArsenate Reductase + Sodium Arsenate From E. coli
ComponentsARSENATE REDUCTASE
KeywordsOXIDOREDUCTASE / ArsC-Cys-12-thioarsenate / Reaction Product Of Arsenate Reductase With 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
: / SULFITE ION / Arsenate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.76 Å
AuthorsMartin, P. / DeMel, S. / Shi, J. / Gladysheva, T. / Gatti, D.L. / Rosen, B.P. / Edwards, B.F.
CitationJournal: Structure / Year: 2001
Title: Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme.
Authors: Martin, P. / DeMel, S. / Shi, J. / Gladysheva, T. / Gatti, D.L. / Rosen, B.P. / Edwards, B.F.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)16,87710
Polymers15,8441
Non-polymers1,0339
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,75420
Polymers31,6882
Non-polymers2,06618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area4130 Å2
ΔGint-295 kcal/mol
Surface area13830 Å2
MethodPISA, PQS
3
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,75420
Polymers31,6882
Non-polymers2,06618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area3900 Å2
ΔGint-285 kcal/mol
Surface area13840 Å2
MethodPISA
4
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,75420
Polymers31,6882
Non-polymers2,06618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area3290 Å2
ΔGint-262 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 86.790, 116.320
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-501-

CS

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Components

#1: Protein ARSENATE REDUCTASE / ARSENICAL PUMP MODIFIER


Mass: 15843.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08692
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical
ChemComp-CS / CESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.05 Å3/Da / Density % sol: 69.16 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 50% saturated Cesium Sulfate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.2 M1dropCs2SO4
2100 mMammonium acetate1droppH4.8
330 mg/mlprotein1drop

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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: Sep 7, 2000 / 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: 1.75→20 Å / Num. all: 26828 / Num. obs: 22762 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 31.74 % / Biso Wilson estimate: 20.094 Å2 / Rmerge(I) obs: 0.1067 / Rsym value: 0.1067 / Net I/σ(I): 21.232
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.02 % / Rmerge(I) obs: 0.3302 / Mean I/σ(I) obs: 8.51 / Num. unique all: 4354 / Rsym value: 0.3302 / % possible all: 40
Reflection
*PLUS
Num. measured all: 722598

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Processing

Software
NameClassification
ARP/wARPmodel building
SHELXL-97refinement
X-GENdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.76→20 Å / Num. parameters: 5596 / Num. restraintsaints: 4714 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 2117 -RANDOM
Rwork0.1641 ---
all-39979 --
obs-39979 84.8 %-
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.015 Å / Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1330.07
Refinement stepCycle: LAST / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 24 234 1347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0306
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.076
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.75→1.88 Å /
RfactorNum. reflection
Rwork0.229 -
obs-4074
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.163 / Rfactor Rfree: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_plane_restr0.031
X-RAY DIFFRACTIONs_chiral_restr0.081

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