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- PDB-1ii0: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ... -

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Basic information

Entry
Database: PDB / ID: 1ii0
TitleCRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE
ComponentsARSENICAL PUMP-DRIVING ATPASE
KeywordsHYDROLASE / ArsA ATPase / 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 / ADENOSINE-5'-TRIPHOSPHATE / : / TRIHYDROXYARSENITE(III) / Arsenical pump-driving ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Conformational changes in four regions of the Escherichia coli ArsA ATPase link ATP hydrolysis to ion translocation.
Authors: Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 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 1.4Feb 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_asym_id / _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_asym_id / _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_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_asym_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_asym_id / _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: ARSENICAL PUMP-DRIVING ATPASE
B: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,54736
Polymers128,1702
Non-polymers4,37734
Water6,305350
1
A: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,31218
Polymers64,0851
Non-polymers2,22717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23518
Polymers64,0851
Non-polymers2,15017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ARSENICAL PUMP-DRIVING ATPASE
B: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules

A: ARSENICAL PUMP-DRIVING ATPASE
B: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,09472
Polymers256,3404
Non-polymers8,75468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area22190 Å2
ΔGint-505 kcal/mol
Surface area87450 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.727, 222.189, 74.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ARSENICAL PUMP-DRIVING ATPASE / ARSENITE-TRANSLOCATING ATPASE / ARSENICAL RESISTANCE ATPASE


Mass: 64084.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARSA / Production host: Escherichia coli (E. coli) / References: UniProt: P08690, EC: 3.6.3.16

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Non-polymers , 7 types, 384 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-TAS / TRIHYDROXYARSENITE(III)


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


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3000, ATP, MgCl2, NaAsO2, CdCl2, Bistrispropane, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 mMADP1drop
31 mM1dropMgCl2
42 mM1dropNaAsO2
51 mM1dropCdCl2
610 mMBis-Tris propane1drop
74 %(w/v)PEG30001reservoir
8100 mMBis-Tris propane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.6 Å / Num. all: 316955 / Num. obs: 316955 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.9
Reflection
*PLUS
Num. obs: 46952 / % possible obs: 90 % / Num. measured all: 316955

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 178177.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4564 10.1 %RANDOM
Rwork0.21 ---
obs0.21 45405 90 %-
all-46952 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å20 Å20 Å2
2---4.03 Å20 Å2
3----0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8425 0 152 350 8927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 485 9.7 %
Rwork0.303 4515 -
obs--60.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3ADP_ATP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMADP_ATP.TOPH
X-RAY DIFFRACTION5ION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.303

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