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- PDB-2olk: ABC Protein ArtP in complex with ADP-beta-S -

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Basic information

Entry
Database: PDB / ID: 2olk
TitleABC Protein ArtP in complex with ADP-beta-S
ComponentsAmino acid ABC transporter
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
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 / P-loop containing nucleoside triphosphate hydrolase ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AT4 / Amino acid ABC transporter
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJan 19, 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 1.3Dec 27, 2023Group: 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
Remark 999Sequence No suitable database references were found at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid ABC transporter
B: Amino acid ABC transporter
C: Amino acid ABC transporter
D: Amino acid ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3948
Polymers117,6204
Non-polymers1,7734
Water9,746541
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.290, 54.117, 106.006
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Amino acid ABC transporter / ATP-binding protein


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: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: D0VWX4*PLUS, polar-amino-acid-transporting ATPase
#2: Chemical
ChemComp-AT4 / 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE / ADENOSINE 5'-O-(2-THIODIPHOSPHATE)


Mass: 443.267 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O9P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 400, 0.1M natrium acetate, 0.1M MES, 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: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2006
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 6.2 / Number: 181241 / Rmerge(I) obs: 0.098 / Χ2: 0.83 / D res high: 2.1 Å / D res low: 40 Å / Num. obs: 54247 / % possible obs: 92.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.524099.410.0661.0073.5
3.594.5299.910.071.0993.7
3.143.5910010.0931.0363.7
2.853.1499.810.140.8793.7
2.652.8599.710.1940.7643.6
2.492.6599.610.2410.6563.4
2.372.4995.110.2720.6283.1
2.262.3786.510.3050.6372.9
2.182.2678.810.3230.6332.8
2.12.1868.710.3810.5782.6
ReflectionResolution: 2.1→40 Å / Num. obs: 54247 / % possible obs: 92.8 % / Observed criterion σ(F): 5 / Redundancy: 3.3 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.098 / Χ2: 0.831 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.66 / Num. unique all: 4006 / Χ2: 0.578 / % possible all: 68.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å28 Å
Translation2.5 Å28 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Complex of ArtP with SO4

Resolution: 2.1→50 Å / FOM work R set: 0.828 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2499 4.3 %RANDOM
Rwork0.204 ---
obs-49832 85.5 %-
Solvent computationBsol: 47.961 Å2
Displacement parametersBiso mean: 37.293 Å2
Baniso -1Baniso -2Baniso -3
1-1.579 Å20 Å2-3.104 Å2
2--9.989 Å20 Å2
3----11.568 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 108 541 8233
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.344
X-RAY DIFFRACTIONc_mcbond_it1.3391.5
X-RAY DIFFRACTIONc_scbond_it2.2372
X-RAY DIFFRACTIONc_mcangle_it2.1342
X-RAY DIFFRACTIONc_scangle_it3.2772.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 49

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.110.375320.329592624
2.11-2.130.335370.308659696
2.13-2.140.305480.294644692
2.14-2.160.342360.284681717
2.16-2.180.292440.294730774
2.18-2.190.323260.264714740
2.19-2.210.285300.267770800
2.21-2.230.288410.257804845
2.23-2.250.318380.259777815
2.25-2.270.231410.279779820
2.27-2.290.318440.272824868
2.29-2.310.28410.255822863
2.31-2.330.282530.254844897
2.33-2.350.303440.258860904
2.35-2.370.235470.241886933
2.37-2.40.262370.238913950
2.4-2.420.313420.238909951
2.42-2.450.298600.257931991
2.45-2.470.269440.2519731017
2.47-2.50.29550.24210091064
2.5-2.530.264520.2459691021
2.53-2.560.275620.2249881050
2.56-2.590.262650.21810121077
2.59-2.630.299700.2159861056
2.63-2.660.293510.21210031054
2.66-2.70.296580.22410751133
2.7-2.740.267620.2329661028
2.74-2.790.286510.24410531104
2.79-2.830.293470.21710641111
2.83-2.880.271420.20510731115
2.88-2.930.274470.22510391086
2.93-2.990.255430.22811031146
2.99-3.050.283470.22410741121
3.05-3.120.306650.23610891154
3.12-3.190.249570.21410891146
3.19-3.270.264470.21610861133
3.27-3.360.23500.17411321182
3.36-3.460.248610.18210701131
3.46-3.570.203620.16411131175
3.57-3.690.237520.18311271179
3.69-3.840.195570.16411351192
3.84-4.020.193500.15910761126
4.02-4.230.202570.16311291186
4.23-4.490.196750.1611161191
4.49-4.840.182660.15411051171
4.84-5.330.183670.17711111178
5.33-6.10.283600.23811301190
6.1-7.680.183600.21811541214
7.68-500.223760.211451221
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
X-RAY DIFFRACTION5ATD.paramATD.top

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