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- PDB-1ii9: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ... -

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Basic information

Entry
Database: PDB / ID: 1ii9
TitleCRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE IN COMPLEX WITH AMP-PNP
ComponentsARSENICAL PUMP-DRIVING ATPASE
KeywordsHYDROLASE / ArsA ATPase / AMP-PNP / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / TRIHYDROXYARSENITE(III) / Arsenical pump-driving ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhou, T. / Radaev, S. / Gatti, D.L. / Rosen, B.P.
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 21, 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: 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.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)132,65737
Polymers128,1702
Non-polymers4,48735
Water4,828268
1
A: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,34619
Polymers64,0851
Non-polymers2,26118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARSENICAL PUMP-DRIVING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,31118
Polymers64,0851
Non-polymers2,22617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.623, 222.527, 74.047
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, 303 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 112.411 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-TAS / TRIHYDROXYARSENITE(III) / Arsenous acid


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


Mass: 18.015 Da / Num. of mol.: 268 / 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: 50.03 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3000, ADP, MgCl2, NaASO2, CdCl2, Bistrispropane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
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: Oct 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→36.52 Å / Num. all: 198246 / Num. obs: 198246 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 5.5
Reflection
*PLUS
Num. obs: 37265 / Num. measured all: 198246

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 301526.59 / 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
Rfree0.265 3725 10 %RANDOM
Rwork0.191 ---
obs0.191 37265 93.5 %-
all-198246 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.62 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-8.12 Å20 Å20 Å2
2---5.91 Å20 Å2
3----2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8365 0 153 268 8786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 581 10.7 %
Rwork0.256 4850 -
obs--83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3ADP_ANP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMADP_ANP.TOP
X-RAY DIFFRACTION5ION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.256

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