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- PDB-1i9d: ARSENATE REDUCTASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1i9d
TitleARSENATE REDUCTASE FROM E. COLI
ComponentsARSENATE REDUCTASE
KeywordsOXIDOREDUCTASE / ARSENIC / ARSENATE / REDUCTASE
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 / MIR / Resolution: 1.65 Å
AuthorsMartin, 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
DepositionMar 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 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 / Item: _software.name
Revision 1.4Feb 7, 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_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_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_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.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_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)17,54715
Polymers15,8491
Non-polymers1,69714
Water6,936385
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)35,09330
Polymers31,6982
Non-polymers3,39528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area6660 Å2
ΔGint-658 kcal/mol
Surface area13210 Å2
MethodPISA
3
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,09330
Polymers31,6982
Non-polymers3,39528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area5030 Å2
ΔGint-493 kcal/mol
Surface area13900 Å2
MethodPISA, PQS
4
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,09330
Polymers31,6982
Non-polymers3,39528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area4350 Å2
ΔGint-478 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.726, 86.726, 116.170
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-602-

CS

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Components

#1: Protein ARSENATE REDUCTASE


Mass: 15849.241 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.: 10 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 3 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 50% Saturated48% Cesium Sulfate, 100 mM Acetate, 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 RUH2R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 17, 2000 / Details: OSMIC
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 55121 / Num. obs: 55121 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 24.6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 209.1
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.7 / % possible all: 87.8
Reflection
*PLUS
% possible obs: 96.9 % / Num. measured all: 1357856

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Processing

Software
NameClassification
SOLVEphasing
PHASESphasing
ARP/wARPmodel building
SHELXLrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.65→20 Å / Num. parameters: 1386 / Num. restraintsaints: 1583 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ENGH AND HUBER
Details: Used full anisotropic refinement with Friedel pairs unmerged.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2878 -RANDOM
Rwork0.134 ---
all0.134 55121 --
obs0.129 55121 100 %-
Refine analyzeOccupancy sum hydrogen: 1111 / Occupancy sum non hydrogen: 1416
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 29 385 1499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_d0.03
Software
*PLUS
Name: 'ARP/WARP, SHELXL' / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_plane_restr0.031
X-RAY DIFFRACTIONs_chiral_restr0.066

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