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- PDB-2v4d: Re-refinement of MexA adaptor protein -

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Basic information

Entry
Database: PDB / ID: 2v4d
TitleRe-refinement of MexA adaptor protein
ComponentsMULTIDRUG RESISTANCE PROTEIN MEXA
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / CELL INNER MEMBRANE / MEXA / MEMBRANE / PALMITATE / TRANSPORT / LIPOPROTEIN / ANTIBIOTIC RESISTANCE / ANTIBIOTIC EFFLUX PUMP / COILED COIL / CELL MEMBRANE / INNER MEMBRANE / PERIPLASMIC ADAPTOR PROTEIN
Function / homology
Function and homology information


efflux transmembrane transporter activity / protein homooligomerization / transmembrane transport / response to antibiotic / identical protein binding / plasma membrane
Similarity search - Function
conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / : / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion ...conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / : / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Multidrug resistance protein MexA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSymmons, M.F. / Bokma, E. / Koronakis, E. / Hughes, C. / Koronakis, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The Assembled Structure of a Complete Tripartite Bacterial Multidrug Efflux Pump.
Authors: Symmons, M.F. / Bokma, E. / Koronakis, E. / Hughes, C. / Koronakis, V.
History
DepositionSep 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MULTIDRUG RESISTANCE PROTEIN MEXA
B: MULTIDRUG RESISTANCE PROTEIN MEXA
C: MULTIDRUG RESISTANCE PROTEIN MEXA
D: MULTIDRUG RESISTANCE PROTEIN MEXA
E: MULTIDRUG RESISTANCE PROTEIN MEXA
F: MULTIDRUG RESISTANCE PROTEIN MEXA
G: MULTIDRUG RESISTANCE PROTEIN MEXA
H: MULTIDRUG RESISTANCE PROTEIN MEXA
I: MULTIDRUG RESISTANCE PROTEIN MEXA
J: MULTIDRUG RESISTANCE PROTEIN MEXA
K: MULTIDRUG RESISTANCE PROTEIN MEXA
L: MULTIDRUG RESISTANCE PROTEIN MEXA
M: MULTIDRUG RESISTANCE PROTEIN MEXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,56429
Polymers502,02713
Non-polymers1,53716
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59430 Å2
ΔGint-297 kcal/mol
Surface area266000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.551, 183.585, 213.314
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MULTIDRUG RESISTANCE PROTEIN MEXA


Mass: 38617.449 Da / Num. of mol.: 13 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52477
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 24 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN G, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN H, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN I, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN J, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN K, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN L, CYS 24 TO SER ENGINEERED RESIDUE IN CHAIN M, CYS 24 TO SER
Sequence detailsSEQUENCE IN STRUCTURE IS OF PROCESSED FORM WHICH HAS 14 RESIDUES REMOVED POST-TRANSLATIONALLY.

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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: 6.09 Å3/Da / Density % sol: 79.65 %
Description: DATASET WAS SAME AS FOR 1T5E REFINEMENT BUT SUBJECT TO XTRIAGE AND RE-SCALING.
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9322
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2003 / Details: MIRRORS
RadiationMonochromator: S1(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 3.2→65.58 Å / Num. obs: 156400 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T5E

1t5e


Resolution: 3.2→65.58 Å / SU ML: 0.43 / σ(F): 0.34 / Phase error: 25.33 / Stereochemistry target values: ML
Details: RESTRAINED B-FACTOR REFINEMENT WAS IN PHENIX 1.3 CONTINUOUS ELECTRON DENSITY FOR RESIDUES 13-28 AND 260-339 WAS OBSERVED ONLY FOR CHAIN F. SIDECHAINS FOR THIS REGION ARE INCLUDED ONLY IN ...Details: RESTRAINED B-FACTOR REFINEMENT WAS IN PHENIX 1.3 CONTINUOUS ELECTRON DENSITY FOR RESIDUES 13-28 AND 260-339 WAS OBSERVED ONLY FOR CHAIN F. SIDECHAINS FOR THIS REGION ARE INCLUDED ONLY IN THIS MOLECULE. OTHER MOLECULES HAD THE POSITION OF THIS REGION MODELLED AS POLY(ALA) BASED ON THE F CHAIN EXAMPLE AND TIGHTLY RESTRAINED TO IT GEOMETRICALLY. THIS REGION COULD NOT BE MODELLED AT ALL IN THE A AND D CHAIN MOLECULES.
RfactorNum. reflection% reflection
Rfree0.264 7669 4.9 %
Rwork0.239 --
obs0.24 156355 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.21 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.9717 Å20 Å24.6583 Å2
2--14.6446 Å2-0 Å2
3---9.2766 Å2
Refinement stepCycle: LAST / Resolution: 3.2→65.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28523 0 80 0 28603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828944
X-RAY DIFFRACTIONf_angle_d1.21239441
X-RAY DIFFRACTIONf_dihedral_angle_d20.55210029
X-RAY DIFFRACTIONf_chiral_restr0.0844615
X-RAY DIFFRACTIONf_plane_restr0.0065375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.32582820.31174906X-RAY DIFFRACTION99
3.2364-3.27450.33772290.29294930X-RAY DIFFRACTION98
3.2745-3.31440.30932540.28224940X-RAY DIFFRACTION100
3.3144-3.35640.30792660.2744908X-RAY DIFFRACTION98
3.3564-3.40050.30642940.26354918X-RAY DIFFRACTION100
3.4005-3.44710.312350.25954886X-RAY DIFFRACTION98
3.4471-3.49630.2922240.24654978X-RAY DIFFRACTION100
3.4963-3.54850.26812660.24134892X-RAY DIFFRACTION98
3.5485-3.6040.2532500.23064996X-RAY DIFFRACTION99
3.604-3.66310.25232330.22354937X-RAY DIFFRACTION99
3.6631-3.72620.22652970.22184891X-RAY DIFFRACTION99
3.7262-3.7940.26942460.21814968X-RAY DIFFRACTION100
3.794-3.86690.25472650.21394913X-RAY DIFFRACTION98
3.8669-3.94580.24082400.21654970X-RAY DIFFRACTION99
3.9458-4.03160.26252620.21324964X-RAY DIFFRACTION100
4.0316-4.12540.25432640.21824914X-RAY DIFFRACTION99
4.1254-4.22860.25792540.21734950X-RAY DIFFRACTION99
4.2286-4.34290.22552450.21014993X-RAY DIFFRACTION99
4.3429-4.47060.23762740.20634961X-RAY DIFFRACTION100
4.4706-4.61490.20962540.20384960X-RAY DIFFRACTION99
4.6149-4.77980.23812630.21214942X-RAY DIFFRACTION99
4.7798-4.97110.26572340.22795009X-RAY DIFFRACTION99
4.9711-5.19730.24162550.23344957X-RAY DIFFRACTION99
5.1973-5.47110.24322430.23284986X-RAY DIFFRACTION99
5.4711-5.81370.26712570.24074974X-RAY DIFFRACTION100
5.8137-6.26230.30642680.26445009X-RAY DIFFRACTION99
6.2623-6.89190.26532480.26855003X-RAY DIFFRACTION99
6.8919-7.88770.27792660.25234980X-RAY DIFFRACTION100
7.8877-9.93210.22592580.19765039X-RAY DIFFRACTION99
9.9321-65.59440.22832430.23425012X-RAY DIFFRACTION97

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