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- PDB-1f48: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ... -

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Basic information

Entry
Database: PDB / ID: 1f48
TitleCRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE
ComponentsARSENITE-TRANSLOCATING ATPASE
KeywordsHYDROLASE / p-loop / antimonite binding site / ATP binding site
Function / homology
Function and homology information


arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Arsenical pump-driving ATPase / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / ANTIMONY (III) ION / TRIHYDROXYANTIMONITE(III) / Arsenical pump-driving ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsZhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump.
Authors: Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: 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 1.4Feb 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Assembly

Deposited unit
A: ARSENITE-TRANSLOCATING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30718
Polymers64,0851
Non-polymers2,22217
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ARSENITE-TRANSLOCATING ATPASE
hetero molecules

A: ARSENITE-TRANSLOCATING ATPASE
hetero molecules

A: ARSENITE-TRANSLOCATING ATPASE
hetero molecules

A: ARSENITE-TRANSLOCATING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,22872
Polymers256,3404
Non-polymers8,88868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area21850 Å2
ΔGint-517 kcal/mol
Surface area87170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.523, 75.715, 222.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-604-

CD

21A-902-

HOH

31A-910-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ARSENITE-TRANSLOCATING ATPASE / ARSA ATPASE


Mass: 64084.992 Da / Num. of mol.: 1 / Fragment: WHOLE PROTEIN WITH C-TERMINAL 6XHISTIDINE TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: R773 / Production host: Escherichia coli (E. coli)
References: UniProt: P08690, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 7 types, 234 molecules

#2: Chemical ChemComp-SB / ANTIMONY (III) ION


Mass: 121.760 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sb
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SBO / TRIHYDROXYANTIMONITE(III)


Mass: 172.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O3Sb
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3000, ADP, magnesium chloride, antimonite, cadmium acetate, Bistrispropane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Details: Zhou, T., (1999) Acta Crystallogr., D55, 921.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 mMADP1drop
31 mM1dropMgCl2
42 mM1dropNaSbO2
51 mM1dropCdCl2
610 mMBis-Tris propane1drop
74 %(w/v)PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 27783 / Num. obs: 27783 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.651 / Num. unique all: 2527 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 178456
Reflection shell
*PLUS
% possible obs: 91.4 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→26.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 430606.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2623 9.9 %RANDOM
Rwork0.206 ---
obs0.206 26510 94.4 %-
all-26510 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.86 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--9.53 Å20 Å2
3----10.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 72 217 4467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_mcbond_it2.951.5
X-RAY DIFFRACTIONc_mcangle_it4.362
X-RAY DIFFRACTIONc_scbond_it4.072
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 386 10.1 %
Rwork0.302 3447 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SB_CL.PARAMSB_CL.TOPH
X-RAY DIFFRACTION3ADP.PARAMADP.TOPH
X-RAY DIFFRACTION4MGCD.PARAMMGCD.TOPH.TOPH
X-RAY DIFFRACTION5WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.302

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