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- PDB-4q4j: Structure of crosslinked TM287/288_S498C_S520C mutant -

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Basic information

Entry
Database: PDB / ID: 4q4j
TitleStructure of crosslinked TM287/288_S498C_S520C mutant
Components
  • ABC transporter
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsHYDROLASE/TRANSPORT PROTEIN / ABC exporter / Multidrug efflux / ABC Transporter / Membrane Transporter / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / 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 transmembrane region fold / ABC transporter type 1, transmembrane domain / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ABC transporter, ATP-binding protein / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHohl, M. / Schoeppe, J. / Gruetter, M.G. / Seeger, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.
Authors: Hohl, M. / Hurlimann, L.M. / Bohm, S. / Schoppe, J. / Grutter, M.G. / Bordignon, E. / Seeger, M.A.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter
B: Uncharacterized ABC transporter ATP-binding protein TM_0288


Theoretical massNumber of molelcules
Total (without water)132,8022
Polymers132,8022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-93 kcal/mol
Surface area50350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.670, 84.140, 113.460
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ABC transporter / ABC transporter / ATP-binding protein / Lipid A export ATP-binding/permease protein MsbA


Mass: 64996.531 Da / Num. of mol.: 1 / Mutation: C28S, C73S, C496S, S498C, C519S, S520C, C598S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287, THEMA_03290, Tmari_0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC3
#2: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 67805.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC4

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 32 % PEG 400, 50 mM Na-Acetate pH 5 and 500 mM KCl, 2.5 mM AMP-PNP, 3 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 33920 / Num. obs: 33360 / % possible obs: 98.35 % / Observed criterion σ(F): -3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.464 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 39.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 1670 5.01 %
Rwork0.2366 --
obs0.2391 33360 98.35 %
all-33920 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9126 0 0 0 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089283
X-RAY DIFFRACTIONf_angle_d1.20112553
X-RAY DIFFRACTIONf_dihedral_angle_d16.553481
X-RAY DIFFRACTIONf_chiral_restr0.0761489
X-RAY DIFFRACTIONf_plane_restr0.0051583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.29430.43841390.39132629X-RAY DIFFRACTION99
3.2943-3.40060.42561370.3672617X-RAY DIFFRACTION98
3.4006-3.52210.36631400.3162668X-RAY DIFFRACTION99
3.5221-3.66310.33791380.26122608X-RAY DIFFRACTION99
3.6631-3.82970.34851390.23922636X-RAY DIFFRACTION99
3.8297-4.03150.31551400.22562640X-RAY DIFFRACTION99
4.0315-4.2840.31111390.21092635X-RAY DIFFRACTION99
4.284-4.61450.25631380.192633X-RAY DIFFRACTION98
4.6145-5.07840.22951390.17922642X-RAY DIFFRACTION98
5.0784-5.81220.28971400.21352664X-RAY DIFFRACTION99
5.8122-7.31880.26691410.27912669X-RAY DIFFRACTION98
7.3188-48.46960.26341400.23682649X-RAY DIFFRACTION95

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