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- PDB-5x5y: A membrane protein complex -

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Basic information

Entry
Database: PDB / ID: 5x5y
TitleA membrane protein complex
Components
  • (Uncharacterized protein) x 2
  • Probable ATP-binding component of ABC transporter
KeywordsMEMBRANE PROTEIN / transporter
Function / homology
Function and homology information


lipopolysaccharide transport / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
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. ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system permease protein LptF / LPS export ABC transporter permease LptG
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.465 Å
AuthorsLuo, Q. / Yang, X. / Huang, Y.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG
Authors: Luo, Q. / Yang, X. / Yu, S. / Shi, H. / Wang, K. / Xiao, L. / Zhu, G. / Sun, C. / Li, T. / Li, D. / Zhang, X. / Zhou, M. / Huang, Y.
History
DepositionFeb 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable ATP-binding component of ABC transporter
A: Probable ATP-binding component of ABC transporter
G: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)134,2134
Polymers134,2134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-57 kcal/mol
Surface area54640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.952, 159.868, 166.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 240 / Label seq-ID: 2 - 240

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBA

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Components

#1: Protein Probable ATP-binding component of ABC transporter


Mass: 27316.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4461 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HVV6
#2: Protein Uncharacterized protein / LptG


Mass: 39235.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA3827 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXH5
#3: Protein Uncharacterized protein / LptF


Mass: 40344.277 Da / Num. of mol.: 1 / Fragment: UNP residues 1-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA3828 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXH4

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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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 277.15 K / Method: evaporation / pH: 7 / Details: PEG 2000, Hepes, magnesium chloride, HEGA-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.46→50 Å / Num. obs: 24569 / % possible obs: 99.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 134.66 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.043 / Rrim(I) all: 0.159 / Χ2: 1.223 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.6310.31.930.5980.612.0280.97897.5
3.63-3.7712.11.4130.820.4141.4741.05598.8
3.77-3.9413.10.9630.9330.2711.13699.3
3.94-4.1513.60.6780.9490.1870.7041.17699.7
4.15-4.41140.4450.9790.1220.4621.32899.9
4.41-4.7514.10.3010.9910.0820.3121.499.9
4.75-5.2314.30.2320.9920.0630.2411.459100
5.23-5.9814.40.2110.9930.0570.2191.32100
5.98-7.5313.90.1440.9970.040.151.258100
7.53-5012.70.0680.9980.020.0710.99299.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QC2

4qc2


Resolution: 3.465→45.641 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 37.99
RfactorNum. reflection% reflection
Rfree0.3039 1195 4.88 %
Rwork0.2692 --
obs0.271 24463 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 237.98 Å2 / Biso mean: 145.7939 Å2 / Biso min: 58.12 Å2
Refinement stepCycle: final / Resolution: 3.465→45.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9178 0 0 0 9178
Num. residues----1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029350
X-RAY DIFFRACTIONf_angle_d0.65212667
X-RAY DIFFRACTIONf_chiral_restr0.0411469
X-RAY DIFFRACTIONf_plane_restr0.0041612
X-RAY DIFFRACTIONf_dihedral_angle_d18.5125587
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2044X-RAY DIFFRACTION18.649TORSIONAL
12B2044X-RAY DIFFRACTION18.649TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4648-3.60350.3751050.30382139224483
3.6035-3.76740.29981280.27862577270599
3.7674-3.9660.30921280.25322594272299
3.966-4.21430.32441420.249425862728100
4.2143-4.53940.27981580.233425982756100
4.5394-4.99570.35631320.230326492781100
4.9957-5.71740.3221310.272326422773100
5.7174-7.19880.33761420.322726712813100
7.1988-45.64540.27441290.27222812294199

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