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- PDB-1z47: Structure of the ATPase subunit CysA of the putative sulfate ATP-... -

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Basic information

Entry
Database: PDB / ID: 1z47
TitleStructure of the ATPase subunit CysA of the putative sulfate ATP-binding cassette (ABC) transporter from Alicyclobacillus acidocaldarius
Componentsputative ABC-transporter ATP-binding protein
KeywordsLIGAND BINDING PROTEIN / alpha/beta motif / beta sandwich
Function / homology
Function and homology information


ABC-type sulfate transporter activity / ATP-binding cassette (ABC) transporter complex / ATP binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #300 / Sulphate transport system permease protein 1 / CysA, C-terminal regulatory domain / CysA C-terminal regulatory domain / Molybdate/tungstate binding, C-terminal / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #300 / Sulphate transport system permease protein 1 / CysA, C-terminal regulatory domain / CysA C-terminal regulatory domain / Molybdate/tungstate binding, C-terminal / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative ABC-transporter ATP-binding protein
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsScheffel, F. / Demmer, U. / Warkentin, E. / Huelsmann, A. / Schneider, E. / Ermler, U.
CitationJournal: Febs Lett. / Year: 2005
Title: Structure of the ATPase subunit CysA of the putative sulfate ATP-binding cassette (ABC) transporter from Alicyclobacillus acidocaldarius
Authors: Scheffel, F. / Demmer, U. / Warkentin, E. / Schneider, E. / Ermler, U.
History
DepositionMar 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 350 GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY ... GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 CHAIN A DOES NOT FORM THE BIOLOGICAL DIMER IN THE CRYSTAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative ABC-transporter ATP-binding protein
B: putative ABC-transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2244
Polymers80,1532
Non-polymers712
Water5,873326
1
B: putative ABC-transporter ATP-binding protein
hetero molecules

B: putative ABC-transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2244
Polymers80,1532
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
A: putative ABC-transporter ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1122
Polymers40,0771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.810, 56.310, 91.620
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsChain B forms the biological dimer. The second part of the biological assembly is generated by the twofold axis: -x, y, -z

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Components

#1: Protein putative ABC-transporter ATP-binding protein / CysA


Mass: 40076.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Gene: cysA / Plasmid: pFSA13 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9RHZ7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.6 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, iospropanol, sodiumcitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 58181 / Num. obs: 58181 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.056 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4300 / Rsym value: 0.155 / % possible all: 69

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1862029.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2944 5.1 %RANDOM
Rwork0.225 ---
all0.23 58076 --
obs0.2251 58076 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7628 Å2 / ksol: 0.384249 e/Å3
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å2-7.48 Å2
2--0.62 Å20 Å2
3----4.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 2 326 5778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 421 5.4 %
Rwork0.274 7366 -
obs-7363 75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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