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- PDB-1j9b: ARSENATE REDUCTASE+0.4M ARSENITE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1j9b
TitleARSENATE REDUCTASE+0.4M ARSENITE 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
: / TRIHYDROXYARSENITE(III) / Arsenate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.26 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
DepositionMay 24, 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 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: 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 / pdbx_initial_refinement_model / 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_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_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)16,7838
Polymers15,9401
Non-polymers8437
Water5,729318
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)33,56616
Polymers31,8802
Non-polymers1,68514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3710 Å2
ΔGint-206 kcal/mol
Surface area13490 Å2
MethodPISA, PQS
3
A: ARSENATE REDUCTASE
hetero molecules

A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,56616
Polymers31,8802
Non-polymers1,68514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area3430 Å2
ΔGint-185 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.613, 86.613, 116.672
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-302-

CS

21A-1301-

HOH

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Components

#1: Protein ARSENATE REDUCTASE


Mass: 15940.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid: R773 / References: UniProt: P08692
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-TAS / TRIHYDROXYARSENITE(III) / Arsenous acid


Mass: 125.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AsH3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 68.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: CESIUM SULFATE, 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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 20, 2000
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.26→20 Å / Num. all: 70105 / Num. obs: 55804 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.155 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 23.6
Reflection shellResolution: 1.26→1.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.4 / Num. unique all: 11094 / Rsym value: 0.684 / % possible all: 34.4
Reflection
*PLUS
Num. obs: 51735 / % possible obs: 90.1 % / Num. measured all: 363771

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Processing

Software
NameClassification
SHELXL-97refinement
XTALVIEWrefinement
XDSdata reduction
X-GENdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NATIVE STRUCTURE

Resolution: 1.26→20 Å / Num. parameters: 13220 / Num. restraintsaints: 15398 / Cross valid method: FREE R / σ(F): 0 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.93%
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 2599 -RANDOM
Rwork0.1342 ---
all0.1397 49199 --
obs0.1276 42030 85.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeLuzzati coordinate error obs: 0.098 Å / Num. disordered residues: 9 / Occupancy sum hydrogen: 1110.55 / Occupancy sum non hydrogen: 1398.83
Refinement stepCycle: LAST / Resolution: 1.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 21 318 1426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0297
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.067
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.096
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor all: 0.14 / Rfactor obs: 0.128 / Rfactor Rfree: 0.166 / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.03
X-RAY DIFFRACTIONs_chiral_restr0.074

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