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- PDB-5mkk: Crystal structure of the heterodimeric ABC transporter TmrAB, a h... -

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Basic information

Entry
Database: PDB / ID: 5mkk
TitleCrystal structure of the heterodimeric ABC transporter TmrAB, a homolog of the antigen translocation complex TAP
Components(Multidrug resistance ABC transporter ATP-binding and permease protein) x 2
KeywordsTRANSPORT PROTEIN / ABC transporter / multidrug resistance / antigenic peptide transporter TAP / lipid transport
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
Multidrug resistance ABC transporter ATP-binding and permease protein / Multidrug resistance ABC transporter ATP-binding and permease protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsNoell, A. / Thomas, C. / Tomasiak, T.M. / Olieric, V. / Wang, M. / Diederichs, K. / Stroud, R.M. / Pos, K.M. / Tampe, R.
Funding support Germany, United States, 4items
OrganizationGrant numberCountry
German Research FoundationSFB 807 Germany
German Research FoundationEXC 115 Germany
National Institutes of HealthGM111126 United States
National Institutes of HealthGM114245 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP.
Authors: Noll, A. / Thomas, C. / Herbring, V. / Zollmann, T. / Barth, K. / Mehdipour, A.R. / Tomasiak, T.M. / Bruchert, S. / Joseph, B. / Abele, R. / Olieric, V. / Wang, M. / Diederichs, K. / Hummer, ...Authors: Noll, A. / Thomas, C. / Herbring, V. / Zollmann, T. / Barth, K. / Mehdipour, A.R. / Tomasiak, T.M. / Bruchert, S. / Joseph, B. / Abele, R. / Olieric, V. / Wang, M. / Diederichs, K. / Hummer, G. / Stroud, R.M. / Pos, K.M. / Tampe, R.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance ABC transporter ATP-binding and permease protein
B: Multidrug resistance ABC transporter ATP-binding and permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7904
Polymers133,5982
Non-polymers1922
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-131 kcal/mol
Surface area51860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.371, 93.371, 1043.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Multidrug resistance ABC transporter ATP-binding and permease protein


Mass: 69095.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0976 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72J05
#2: Protein Multidrug resistance ABC transporter ATP-binding and permease protein


Mass: 64503.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0977 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72J04
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.92 Å3/Da / Density % sol: 74.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 26-30% PEG 400, 0.1 M Na3Citrate/HCl pH 3.5, 0.1 M Li2SO4, 0-2.5 mM CYMAL-5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.9 Å / Num. obs: 77034 / % possible obs: 100 % / Redundancy: 17.7 % / CC1/2: 0.997 / Rrim(I) all: 0.11 / Net I/σ(I): 16.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.276 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.9 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.39
RfactorNum. reflection% reflection
Rfree0.2715 3853 5 %
Rwork0.2261 --
obs0.2284 77034 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9291 0 10 10 9311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089492
X-RAY DIFFRACTIONf_angle_d1.14112864
X-RAY DIFFRACTIONf_dihedral_angle_d15.3933489
X-RAY DIFFRACTIONf_chiral_restr0.0421469
X-RAY DIFFRACTIONf_plane_restr0.0051633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73290.42561350.36012554X-RAY DIFFRACTION100
2.7329-2.76750.41621320.34382515X-RAY DIFFRACTION100
2.7675-2.80390.33161350.32762554X-RAY DIFFRACTION100
2.8039-2.84230.36811340.30792560X-RAY DIFFRACTION100
2.8423-2.88290.35551330.29982518X-RAY DIFFRACTION100
2.8829-2.9260.33261360.2882578X-RAY DIFFRACTION100
2.926-2.97170.31661320.27062514X-RAY DIFFRACTION100
2.9717-3.02040.31961360.27132580X-RAY DIFFRACTION100
3.0204-3.07250.31011320.27222506X-RAY DIFFRACTION100
3.0725-3.12830.33031380.28272628X-RAY DIFFRACTION100
3.1283-3.18850.3331320.27912501X-RAY DIFFRACTION100
3.1885-3.25360.30061360.26052589X-RAY DIFFRACTION100
3.2536-3.32430.27081360.24192582X-RAY DIFFRACTION100
3.3243-3.40160.28011340.24412550X-RAY DIFFRACTION100
3.4016-3.48660.29581360.22662582X-RAY DIFFRACTION100
3.4866-3.58090.25181390.22812633X-RAY DIFFRACTION100
3.5809-3.68620.25161340.22432554X-RAY DIFFRACTION100
3.6862-3.80520.27221350.22572567X-RAY DIFFRACTION100
3.8052-3.94110.26771390.21192640X-RAY DIFFRACTION100
3.9411-4.09880.23661370.19142592X-RAY DIFFRACTION100
4.0988-4.28530.24741390.19432644X-RAY DIFFRACTION100
4.2853-4.51110.21291380.18352628X-RAY DIFFRACTION100
4.5111-4.79350.23551390.16562634X-RAY DIFFRACTION100
4.7935-5.16320.19481420.16672702X-RAY DIFFRACTION100
5.1632-5.68210.25331400.1872657X-RAY DIFFRACTION100
5.6821-6.50270.27011440.22612749X-RAY DIFFRACTION100
6.5027-8.18640.28861480.24152806X-RAY DIFFRACTION100
8.1864-48.91280.30511620.26523064X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09730.21910.27280.60550.28120.69540.05780.0770.0648-0.7369-0.24410.06930.43110.24910.04871.08750.29180.02161.0579-0.27580.7026.505632.4835-51.9663
22.26851.089-0.45221.18240.3221.34250.0271-0.0850.2606-0.0056-0.13760.1470.1153-0.21930.08310.60370.02610.00240.6593-0.30940.8922-0.708466.3426-7.6337
30.3413-0.35820.30050.3735-0.17470.54630.36110.3040.0835-0.7794-0.0656-0.4240.1285-0.11370.07041.19010.15810.24040.9364-0.37860.777420.207228.7845-43.649
41.53920.29260.59282.23050.51991.6752-0.13040.2528-0.1393-0.1517-0.01720.1488-0.27750.0012-0.01830.4443-0.03180.01210.7243-0.28270.7228-3.367331.80066.6784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 331 )
2X-RAY DIFFRACTION2chain 'A' and (resid 332 through 603 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 317 )
4X-RAY DIFFRACTION4chain 'B' and (resid 318 through 578 )

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