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- PDB-5idv: Structure of the nucleotide binding domain of an ABC transporter ... -

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Basic information

Entry
Database: PDB / ID: 5idv
TitleStructure of the nucleotide binding domain of an ABC transporter MsbA from Acinetobacter baumannii
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsTRANSPORT PROTEIN / SSGCID / Acinetobacter baumannii / MsbA / nucleotide binding domain / ATP-binding / Lipid A export / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesAcinetobacter baumannii AB5075 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of the nucleotide binding domain of an ABC transporter MsbA from Acinetobacter baumannii
Authors: Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid A export ATP-binding/permease protein MsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1533
Polymers31,0291
Non-polymers1242
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipid A export ATP-binding/permease protein MsbA
hetero molecules

A: Lipid A export ATP-binding/permease protein MsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3066
Polymers62,0582
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4470 Å2
ΔGint-23 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.220, 89.030, 104.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

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


Mass: 31028.783 Da / Num. of mol.: 1 / Fragment: AcbaC.18886.a.B2 (UNP residues 305-575)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: msbA, APC40_11520 / Plasmid: AcbaC.18886.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0Q2LVW2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.44 Å3/Da / Density % sol: 49.59 % / Mosaicity: 0.22 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ A8 (267191a8): 200mM Ammonium formate, 20% PEG3350; protein conc. 17.3mg/mL; 20% ethylene glycol cryo; puck aak7-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→52.613 Å / Num. obs: 53798 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.14 % / Biso Wilson estimate: 23.521 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.496.080.5393.171100
1.49-1.530.4174.061100
1.53-1.570.3215.341100
1.57-1.620.2636.53199.9
1.62-1.670.2118.14199.9
1.67-1.730.16810.21100
1.73-1.80.13712.31100
1.8-1.870.09916.88199.9
1.87-1.960.07421.941100
1.96-2.050.05926.74199.9
2.05-2.160.04733.17199.9
2.16-2.290.0438.35199.9
2.29-2.450.03542.49199.8
2.45-2.650.03345.76199.7
2.65-2.90.02953.09199.5
2.9-3.240.02658.98199.3
3.24-3.740.02366.47198.6
3.74-4.590.0270.2198.5
4.59-6.480.01969.28197.9
6.48-52.6130.01966.58192

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
PHENIXdev_2313refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QLA

4qla


Resolution: 1.45→50 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.7
RfactorNum. reflection% reflection
Rfree0.178 1998 3.72 %
Rwork0.149 --
obs0.1501 53760 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.98 Å2 / Biso mean: 22.9851 Å2 / Biso min: 9.95 Å2
Refinement stepCycle: final / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 8 290 2327
Biso mean--21.16 34.85 -
Num. residues----263

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