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- PDB-4rhb: Crystal structure of the lipopolysaccharide assembly complex LptD... -

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Basic information

Entry
Database: PDB / ID: 4rhb
TitleCrystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
KeywordsTRANSPORT PROTEIN / lipopolysaccharide assembly / lipid binding protein / outer membrane of Gram-negative bacteria / 26-stranded beta barrel and 2-layer beta sandwich
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
Lipoprotein like domain / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain ...Lipoprotein like domain / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.355 Å
AuthorsMalojcic, G. / Garner, R.A. / Kahne, D.
CitationJournal: To be Published
Title: Structural basis of lipopolysaccharide insertion into the bacterial outer membrane
Authors: Malojcic, G. / Garner, R.A. / Kahne, D.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,5909
Polymers181,4254
Non-polymers1655
Water724
1
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7714
Polymers90,7132
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-31 kcal/mol
Surface area32830 Å2
MethodPISA
2
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8195
Polymers90,7132
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-28 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.040, 136.620, 108.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELEULEUAA230 - 78452 - 606
21ILEILELEULEUCC230 - 78452 - 606
12GLYGLYSERSERBB20 - 1692 - 151
22GLYGLYSERSERDD20 - 1692 - 151

NCS ensembles :
ID
1
2

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Components

#1: Protein LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 71233.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lptD, imp, ostA, yabG, b0054, JW0053 / Production host: Escherichia coli (E. coli) / References: UniProt: P31554
#2: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 19479.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.61 Å3/Da / Density % sol: 52.89 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.355→200 Å / Num. all: 27863 / Num. obs: 26835 / % possible obs: 96.3 % / Observed criterion σ(I): 0.47

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q35

4q35


Resolution: 3.355→108.31 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / SU B: 57.935 / SU ML: 0.843 / Cross valid method: THROUGHOUT / ESU R Free: 0.786 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3378 1250 4.7 %RANDOM
Rwork0.25668 ---
obs0.2606 25585 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 115.877 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2--1.34 Å20 Å2
3----5.32 Å2
Refinement stepCycle: LAST / Resolution: 3.355→108.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11498 0 5 4 11507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211910
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210699
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9316209
X-RAY DIFFRACTIONr_angle_other_deg0.913324517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.67951433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13523.976654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.812151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9511592
X-RAY DIFFRACTIONr_chiral_restr0.0790.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213907
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023041
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_it8.28911.4175690
X-RAY DIFFRACTIONr_mcbond_other8.28911.4175689
X-RAY DIFFRACTIONr_mcangle_it13.21617.0977119
X-RAY DIFFRACTIONr_mcangle_other13.7617.2027135
X-RAY DIFFRACTIONr_scbond_it7.64911.9496220
X-RAY DIFFRACTIONr_scbond_other8.01812.0546240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.99417.8759115
X-RAY DIFFRACTIONr_long_range_B_refined18.88992.40713617
X-RAY DIFFRACTIONr_long_range_B_other18.88992.41113618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A318750.07
12C318750.07
21B90250.06
22D90250.06
LS refinement shellResolution: 3.355→3.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 75 -
Rwork0.407 1478 -
obs--77.03 %

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