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- PDB-4mlb: Reverse polarity of binding pocket suggests different function of... -

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Basic information

Entry
Database: PDB / ID: 4mlb
TitleReverse polarity of binding pocket suggests different function of a MOP superfamily transporter from Pyrococcus furiosus Vc1 (DSM3638)
ComponentsPF0708
KeywordsTRANSPORT PROTEIN / lipid translocase / flippase / membrane protein
Function / homology: / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / PENTAETHYLENE GLYCOL MONODECYL ETHER / MATE family efflux transporter
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å
AuthorsMalviya, V.N. / Nonaka, T. / Muenke, C. / Koepke, J. / Michel, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Inward-facing conformation of a multidrug resistance MATE family transporter.
Authors: Zakrzewska, S. / Mehdipour, A.R. / Malviya, V.N. / Nonaka, T. / Koepke, J. / Muenke, C. / Hausner, W. / Hummer, G. / Safarian, S. / Michel, H.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Structure summary
Revision 1.2Sep 12, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PF0708
B: PF0708
C: PF0708
D: PF0708
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,84659
Polymers211,7134
Non-polymers20,13455
Water5,891327
1
A: PF0708
C: PF0708
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,41937
Polymers105,8562
Non-polymers12,56335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint84 kcal/mol
Surface area23610 Å2
2
B: PF0708
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,47113
Polymers52,9281
Non-polymers4,54312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PF0708
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,98517
Polymers52,9281
Non-polymers6,05716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PF0708
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9569
Polymers52,9281
Non-polymers3,0288
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.560, 94.548, 138.822
Angle α, β, γ (deg.)90.00, 126.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PF0708


Mass: 52928.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2X0
#2: Chemical...
ChemComp-CXE / PENTAETHYLENE GLYCOL MONODECYL ETHER


Mass: 378.544 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: C20H42O6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml protein, 0.1 M ADA/NaOH, pH 6.5, 10 mM ytterbium chloride, 0.15% w/v OG-Se, 24% w/v PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.17 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.17 Å / Relative weight: 1
ReflectionResolution: 2.349→47.27 Å / Num. all: 95646 / Num. obs: 95103 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14
Reflection shellResolution: 2.349→2.48 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MKT

3mkt


Resolution: 2.349→45.24 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4737 4.98 %RANDOM
Rwork0.2026 ---
obs0.2041 95091 99.73 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.304 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1931 Å2-0 Å2-3.3073 Å2
2---2.2666 Å2-0 Å2
3----3.9265 Å2
Refinement stepCycle: LAST / Resolution: 2.349→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13621 0 761 327 14709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314616
X-RAY DIFFRACTIONf_angle_d0.79419524
X-RAY DIFFRACTIONf_dihedral_angle_d16.7365525
X-RAY DIFFRACTIONf_chiral_restr0.052312
X-RAY DIFFRACTIONf_plane_restr0.0042308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.349-2.37560.30341260.27542922X-RAY DIFFRACTION98
2.3756-2.40350.32131810.24812969X-RAY DIFFRACTION100
2.4035-2.43280.28421400.24543075X-RAY DIFFRACTION100
2.4328-2.46360.30741710.23712943X-RAY DIFFRACTION100
2.4636-2.49610.29621810.23553030X-RAY DIFFRACTION100
2.4961-2.53020.29941330.22753001X-RAY DIFFRACTION100
2.5302-2.56640.29381570.2212992X-RAY DIFFRACTION100
2.5664-2.60470.25811610.21423017X-RAY DIFFRACTION100
2.6047-2.64540.28011500.21573030X-RAY DIFFRACTION100
2.6454-2.68880.25961730.22322950X-RAY DIFFRACTION100
2.6888-2.73510.28871520.2172997X-RAY DIFFRACTION100
2.7351-2.78480.25531620.21553037X-RAY DIFFRACTION100
2.7848-2.83840.25751440.20673023X-RAY DIFFRACTION100
2.8384-2.89630.24661810.20283029X-RAY DIFFRACTION100
2.8963-2.95930.27611520.20462978X-RAY DIFFRACTION100
2.9593-3.02810.24381420.2063027X-RAY DIFFRACTION100
3.0281-3.10380.24051550.20512995X-RAY DIFFRACTION100
3.1038-3.18770.2431660.20513014X-RAY DIFFRACTION100
3.1877-3.28150.23861720.2052992X-RAY DIFFRACTION100
3.2815-3.38740.23791330.20373061X-RAY DIFFRACTION100
3.3874-3.50840.22931590.19273021X-RAY DIFFRACTION100
3.5084-3.64880.20112000.19472971X-RAY DIFFRACTION100
3.6488-3.81480.2321070.18523046X-RAY DIFFRACTION100
3.8148-4.01580.22071780.18893007X-RAY DIFFRACTION100
4.0158-4.26720.20062130.18012974X-RAY DIFFRACTION100
4.2672-4.59640.2218300.18253155X-RAY DIFFRACTION100
4.5964-5.05840.22942420.1912918X-RAY DIFFRACTION100
5.0584-5.78910.27562400.22872971X-RAY DIFFRACTION100
5.7891-7.288700.21943235X-RAY DIFFRACTION100
7.2887-45.24850.14812360.18382974X-RAY DIFFRACTION98

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