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- PDB-5l75: A protein structure -

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Basic information

Entry
Database: PDB / ID: 5l75
TitleA protein structure
Components
  • FIG000906: Predicted Permease
  • FIG000988: Predicted permease
  • Lipopolysaccharide ABC transporter, ATP-binding protein LptB
KeywordsTRANSPORT PROTEIN / Gram-negative bacteria
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding
Similarity search - Function
Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Lipopolysaccharide ABC transporter, ATP-binding protein LptB / FIG000988: Predicted permease / FIG000906: Predicted Permease
Similarity search - Component
Biological speciesKlebsiella pneumoniae IS22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å
AuthorsDong, C. / Dong, H. / Zhang, Z. / Paterson, N. / Tang, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG.
Authors: Dong, H. / Zhang, Z. / Tang, X. / Paterson, N.G. / Dong, C.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide ABC transporter, ATP-binding protein LptB
B: Lipopolysaccharide ABC transporter, ATP-binding protein LptB
F: FIG000988: Predicted permease
G: FIG000906: Predicted Permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2946
Polymers133,9044
Non-polymers3902
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-107 kcal/mol
Surface area54220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.259, 210.521, 258.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Lipopolysaccharide ABC transporter, ATP-binding protein LptB


Mass: 26879.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae IS22 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1B6A5
#2: Protein FIG000988: Predicted permease


Mass: 40481.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae IS22 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1B830
#3: Protein FIG000906: Predicted Permease


Mass: 39662.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae IS22 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1B8C5
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt

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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: 5.36 Å3/Da / Density % sol: 77.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 mM MES pH 6.5, 0.1 M sodium chloride, 0.1 M Lithium sulfate and 24% PEG 300

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Apr 10, 2016
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.7→29.96 Å / Num. obs: 1198560 / % possible obs: 99.8 % / Observed criterion σ(I): 1.7 / Redundancy: 120 % / Biso Wilson estimate: 110.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.262 / Net I/σ(I): 15.5
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 117.5 % / Rmerge(I) obs: 1.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.7→29.96 Å / Cor.coef. Fo:Fc: 0.74 / Cor.coef. Fo:Fc free: 0.771 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.876
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1041 5.13 %RANDOM
Rwork0.284 ---
obs0.286 20311 65.3 %-
Displacement parametersBiso mean: 112.77 Å2
Baniso -1Baniso -2Baniso -3
1--325.8464 Å20 Å20 Å2
2--210.6615 Å20 Å2
3---115.1849 Å2
Refine analyzeLuzzati coordinate error obs: 0.74 Å
Refinement stepCycle: 1 / Resolution: 3.7→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8822 0 2 0 8824
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098974HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1112146HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3148SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1302HARMONIC5
X-RAY DIFFRACTIONt_it8974HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion23.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1180SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10697SEMIHARMONIC4
LS refinement shellResolution: 3.7→3.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.368 109 6.25 %
Rwork0.34 1635 -
all0.341 1744 -
obs--38.77 %

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