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- PDB-6bl6: Crystallization of lipid A transporter MsbA from Salmonella typhi... -

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Basic information

Entry
Database: PDB / ID: 6bl6
TitleCrystallization of lipid A transporter MsbA from Salmonella typhimurium: a novel perspective on its transport
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsMEMBRANE PROTEIN / MsbA / Lipid A co-crystallization / ABC transporters / Staphylococcus typhimurium
Function / homologyABC transporter, conserved site / ABC transporter / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, lipid A export, MsbA ...ABC transporter, conserved site / ABC transporter / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, lipid A export, MsbA / ABC transporter transmembrane region / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / Type I protein exporter / ABC-type lipid A-core oligosaccharide transporter / lipid-transporting ATPase activity / integral component of membrane / ATP binding / identical protein binding / plasma membrane / Lipid A export ATP-binding/permease protein MsbA
Function and homology information
Specimen sourceSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.8 Å resolution
AuthorsPadayatti, P.S. / Zhang, Q. / Wilson, I.A. / Lee, S.C.
CitationJournal: To be published
Title: Crystallization of lipid A transporter MsbA from Salmonella typhimurium: a novel perspective on its transport
Authors: Padayatti, P.S. / Zhang, Q.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2017 / Release: Jan 9, 2019
RevisionDateData content typeGroupCategoryProviderType
1.0Jan 9, 2019Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelAuthor supporting evidence / Data collection / Structure summaryaudit_author / pdbx_audit_support

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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
B: Lipid A export ATP-binding/permease protein MsbA


Theoretical massNumber of molelcules
Total (without water)127,2152
Polyers127,2152
Non-polymers00
Water0
1
A: Lipid A export ATP-binding/permease protein MsbA

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


Theoretical massNumber of molelcules
Total (without water)127,2152
Polyers127,2152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area (Å2)10450
ΔGint (kcal/M)-98
Surface area (Å2)54180
MethodPISA
2
B: Lipid A export ATP-binding/permease protein MsbA

B: Lipid A export ATP-binding/permease protein MsbA


Theoretical massNumber of molelcules
Total (without water)127,2152
Polyers127,2152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area (Å2)10360
ΔGint (kcal/M)-97
Surface area (Å2)54390
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)82.052, 154.819, 228.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

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


Mass: 63607.566 Da / Num. of mol.: 2
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: msbA, STM0984 / Variant: SGSC1412 / Plasmid name: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63359, Hydrolases, Acting on acid anhydrides, Acting on acid anhydrides to catalyse transmembrane movement of substances

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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: 5.71 / Density percent sol: 78.47 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MsbA purified in detergent micelles (UDM/FA231) is mixed with lipid A prior to crystallization and mixed 1: 1 with well solution 20 mM Tris-Hcl (pH 7.5) and 15-20 5 PEG 300 . Crystals appeared in month (approx.)
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 80 kelvins / Ambient temp details: 80
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Jan 28, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127085 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 68.3 Å2 / D resolution high: 2.8 Å / D resolution low: 50.01 Å / Number obs: 60504 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / CC half: 0.893 / Rmerge I obs: 0.136 / Rpim I all: 0.057 / Rrim I all: 0.148 / Chi squared: 1.288 / NetI over av sigmaI: 1 / NetI over sigmaI: 10 / Redundancy: 5 % / Percent possible obs: 84.9
Reflection shellRmerge I obs: 0.136 / Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / Rpim I all: 0.057 / Redundancy: 4.1 % / Percent possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B5W
Correlation coeff Fo to Fc: 0.937 / Correlation coeff Fo to Fc free: 0.925 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 23.048 / Overall SU ML: 0.381 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.519 / Overall ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 116.187 Å2 / Aniso B11: 6.23 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 8.18 Å2 / Aniso B23: - Å2 / Aniso B33: -14.41 Å2
Least-squares processR factor R free: 0.30071 / R factor R work: 0.26951 / R factor obs: 0.27104 / Highest resolution: 2.8 Å / Lowest resolution: 50.01 Å / Number reflection R free: 2963 / Number reflection obs: 57572 / Percent reflection R free: 4.9 / Percent reflection obs: 82.87
Refine hist #1Highest resolution: 2.8 Å / Lowest resolution: 50.01 Å
Number of atoms included #1Protein: 8894 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 8894
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199028
X-RAY DIFFRACTIONr_bond_other_d0.0010.0208756
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.96412202
X-RAY DIFFRACTIONr_angle_other_deg0.9743.00020190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2005.0001148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81823.370368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22215.0001644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.49415.00072
X-RAY DIFFRACTIONr_chiral_restr0.0770.2001452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0209944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0201840
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.93211.4724598
X-RAY DIFFRACTIONr_mcbond_other6.93311.4724597
X-RAY DIFFRACTIONr_mcangle_it10.57817.2305744
X-RAY DIFFRACTIONr_mcangle_other10.57717.2315745
X-RAY DIFFRACTIONr_scbond_it6.84012.2124430
X-RAY DIFFRACTIONr_scbond_other6.83912.2124431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.83418.0116459
X-RAY DIFFRACTIONr_long_range_B_refined14.3549977
X-RAY DIFFRACTIONr_long_range_B_other14.3509975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints ncs

Ens ID: 1 / Number: 35750 / Refine ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom IDAuth asym ID
1A
2B
Refine LS shellHighest resolution: 2.796 Å / R factor R free: 0.526 / R factor R work: 0.536 / Lowest resolution: 2.868 Å / Number reflection R free: 194 / Number reflection R work: 3269 / Total number of bins used: 20 / Percent reflection obs: 65.14

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