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- PDB-6u94: Structure of RND efflux system, outer membrane lipoprotein, NodT ... -

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Basic information

Entry
Database: PDB / ID: 6u94
TitleStructure of RND efflux system, outer membrane lipoprotein, NodT family from Burkholderia mallei ATCC 23344
ComponentsRND efflux system, outer membrane lipoprotein, NodT family
KeywordsLIPID TRANSPORT / outer membrane lipoprotein / NodT family / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


efflux transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RND efflux system, outer membrane lipoprotein, NodT family
Similarity search - Component
Biological speciesBurkholderia mallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHoranyi, P.S. / Fox III, D. / Abendroth, J. / Lorimer, D. / Edwards, T. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Structure of RND efflux system, outer membrane lipoprotein, NodT family from Burkholderia mallei ATCC 23344
Authors: Horanyi, P.S. / Fox III, D. / Abendroth, J. / Lorimer, D. / Edwards, T.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RND efflux system, outer membrane lipoprotein, NodT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2454
Polymers63,9691
Non-polymers2763
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-3 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.440, 93.440, 370.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein RND efflux system, outer membrane lipoprotein, NodT family


Mass: 63968.863 Da / Num. of mol.: 1 / Fragment: UNP residues 28-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia mallei (strain ATCC 23344) (bacteria)
Strain: ATCC 23344 / Gene: BMAA1392 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2WCA9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30 mM magnesium chloride hexahydrate, 30 mM calcium chloride dihydrate, 0.1 M Tris base, BICINE, pH 8.5, 20% v/v ethylene glycol, 10% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 18, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→30.48 Å / Num. obs: 26543 / % possible obs: 99.8 % / Redundancy: 7.36 % / CC1/2: 0.99 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.5
Reflection shellResolution: 2.35→2.4 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 1932 / CC1/2: 0.972

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D5K

3d5k


Resolution: 2.35→30.48 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs26410 99.42 %
Displacement parametersBiso mean: 82.67 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 18 44 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222931
X-RAY DIFFRACTIONf_angle_d0.42493989
X-RAY DIFFRACTIONf_chiral_restr0.032471
X-RAY DIFFRACTIONf_plane_restr0.0027527
X-RAY DIFFRACTIONf_dihedral_angle_d11.46561752

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