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- PDB-2ouk: ABC Protein ArtP in complex with Sulphate -

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Basic information

Entry
Database: PDB / ID: 2ouk
TitleABC Protein ArtP in complex with Sulphate
Componentsprotein ArtP
KeywordsHYDROLASE / ABC Domain / ATPase
Function / homology
Function and homology information


polar-amino-acid-transporting ATPase / ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
ABC-type amino acid transport system, ATPase component, HisP-type / : / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain ...ABC-type amino acid transport system, ATPase component, HisP-type / : / 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. / 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
Amino acid ABC transporter
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsThaben, P.F. / Eckey, V. / Scheffel, F. / Saenger, W. / Schneider, E. / Vahedi-Faridi, A.
CitationJournal: To be Published
Title: Crystal structures of the ATP-binding cassette (ABC) protein ArtP from Geobacillus stearothermophilus reveal a stable dimer in the post hydrolysis state and an asymmetry in the dimerization region
Authors: Thaben, P.F. / Eckey, V. / Scheffel, F. / Saenger, W. / Schneider, E. / Vahedi-Faridi, A.
History
DepositionFeb 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein ArtP
B: protein ArtP
C: protein ArtP
D: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,19710
Polymers117,6204
Non-polymers5766
Water9,404522
1
A: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5012
Polymers29,4051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5973
Polymers29,4051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5012
Polymers29,4051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5973
Polymers29,4051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: protein ArtP
B: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0985
Polymers58,8102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: protein ArtP
D: protein ArtP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0985
Polymers58,8102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.164, 80.628, 95.584
Angle α, β, γ (deg.)90.000, 104.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
protein ArtP / E.C.3.6.3.21 / Amino acid ABC transporter


Mass: 29405.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: DSMZ 13240 / Gene: artP / Plasmid: pVE6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: D0VWX4*PLUS, polar-amino-acid-transporting ATPase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 23% PEG 3350, 0.1M BisTris, 0,2M lithium sulphate, 1,5% CAPB (TEGO BetainF), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97973 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 28, 2006
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 55290 / % possible obs: 94.2 % / Observed criterion σ(F): 5 / Redundancy: 3.3 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.813 / Net I/σ(I): 7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.45 / Num. unique all: 4714 / Χ2: 0.575 / % possible all: 80.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å42.87 Å
Translation2.5 Å42.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODEL GENERATED MODEL

Resolution: 2.15→50 Å / FOM work R set: 0.812 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2625 4.5 %RANDOM
Rwork0.211 ---
obs-51803 88.2 %-
Solvent computationBsol: 39.64 Å2
Displacement parametersBiso mean: 32.592 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å2-5.613 Å2
2--1.557 Å20 Å2
3---0.472 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7568 0 30 522 8120
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.251
X-RAY DIFFRACTIONc_mcbond_it1.3581.5
X-RAY DIFFRACTIONc_scbond_it2.1552
X-RAY DIFFRACTIONc_mcangle_it2.1822
X-RAY DIFFRACTIONc_scangle_it3.2052.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.15-2.160.344440.311607651
2.16-2.180.296340.317697731
2.18-2.190.377400.298798838
2.19-2.210.305410.285819860
2.21-2.230.371400.295875915
2.23-2.240.328470.289821868
2.24-2.260.345430.287864907
2.26-2.280.404350.295880915
2.28-2.30.358510.29847898
2.3-2.320.3470.26867914
2.32-2.340.346480.274882930
2.34-2.360.361520.264900952
2.36-2.380.334460.269914960
2.38-2.40.312490.256911960
2.4-2.420.404440.274917961
2.42-2.440.292330.264916949
2.44-2.470.302510.249900951
2.47-2.490.251430.24950993
2.49-2.520.299600.24921981
2.52-2.550.333480.257927975
2.55-2.580.313570.262934991
2.58-2.610.303510.2499921043
2.61-2.640.257600.2339651025
2.64-2.670.251410.2410041045
2.67-2.710.363690.2529671036
2.71-2.750.337530.259771030
2.75-2.790.302490.24410221071
2.79-2.830.281550.2410161071
2.83-2.870.344500.24110421092
2.87-2.920.254420.21410611103
2.92-2.970.263570.20910311088
2.97-3.020.273570.21110391096
3.02-3.080.333620.22910981160
3.08-3.140.272570.22210511108
3.14-3.210.287670.23311171184
3.21-3.290.22790.210731152
3.29-3.370.2610.17510841145
3.37-3.460.224650.18910951160
3.46-3.560.232630.18810961159
3.56-3.680.231560.18911321188
3.68-3.810.224470.18111111158
3.81-3.960.222520.18210881140
3.96-4.140.238570.17111121169
4.14-4.360.222670.16511171184
4.36-4.630.185650.15510881153
4.63-4.990.208650.16911201185
4.99-5.490.216660.19511041170
5.49-6.280.26530.2111321185
6.28-7.910.21550.18911341189
7.91-500.187510.18111631214
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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