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- PDB-4n4r: Structure basis of lipopolysaccharide biogenesis -

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Basic information

Entry
Database: PDB / ID: 4n4r
TitleStructure basis of lipopolysaccharide biogenesis
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
KeywordsMEMBRANE PROTEIN / Beta barrel / Translocase / Lipopolysaccharide transport proteins
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
CACODYLATE ION / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsDong, H. / Xiang, Q. / Wang, Z. / Paterson, N.G. / He, C. / Zhang, Y. / Wang, W. / Dong, C.
CitationJournal: Nature / Year: 2014
Title: Structural basis for outer membrane lipopolysaccharide insertion.
Authors: Dong, H. / Xiang, Q. / Gu, Y. / Wang, Z. / Paterson, N.G. / Stansfeld, P.J. / He, C. / Zhang, Y. / Wang, W. / Dong, C.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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_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)225,8168
Polymers225,4124
Non-polymers4054
Water18010
1
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9084
Polymers112,7062
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-14 kcal/mol
Surface area32140 Å2
MethodPISA
2
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9084
Polymers112,7062
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-11 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.430, 76.082, 213.596
Angle α, β, γ (deg.)90.00, 111.52, 90.00
Int Tables number5
Space group name H-MI121
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
11SERSERMSEMSEAA226 - 786226 - 786
21SERSERMSEMSECC226 - 786226 - 786
12CYSCYSALAALABB19 - 16919 - 169
22CYSCYSALAALADD19 - 16919 - 169

NCS ensembles :
ID
1
2

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Components

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


Mass: 90852.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2/ SGSC1412 / ATCC 700720 / Gene: imp, lptD, ostA, STM0093 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q8ZRW0
#2: Protein LPS-assembly lipoprotein LptE


Mass: 21853.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: lptE, rlpB, STM0647 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q8ZQZ7
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M zinc acetate, 0.1M sodium cacodylate, 18% PEG8000 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97887, 0.97835, 0.98181, 0.97750
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.978351
30.981811
40.97751
ReflectionResolution: 2.8→107.49 Å / Num. obs: 64252 / % possible obs: 9.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.6 / Redundancy: 5.6 % / Rmerge(I) obs: 0.154 / Rsym value: 0.16 / Net I/σ(I): 1.6
Reflection shellResolution: 2.8→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.93 / % possible all: 94

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Processing

Software
NameVersionClassification
EDNAdata collection
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→107.49 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.907 / SU B: 44.165 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.667 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30508 3253 5.1 %RANDOM
Rwork0.28535 ---
obs0.28638 60999 99.83 %-
all-67200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.272 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-0 Å2-0.84 Å2
2--5.33 Å2-0 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.02 Å0.02 Å
Luzzati d res low-7 Å
Luzzati sigma a0.6 Å0.025 Å
Refinement stepCycle: LAST / Resolution: 2.8→107.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11095 0 12 10 11117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.94315455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49951357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.42824.18610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.706151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5831578
X-RAY DIFFRACTIONr_chiral_restr0.1190.21631
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218918
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.448311328
X-RAY DIFFRACTIONr_sphericity_free74.20459
X-RAY DIFFRACTIONr_sphericity_bonded38.785511064
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7710.1
12C7710.1
21B1810.19
22D1810.19
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 223 -
Rwork0.523 4287 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77520.0523-0.37910.2901-0.44981.7315-0.07140.4820.08670.07490.12330.0245-0.11460.1331-0.05190.7074-0.04410.00440.6519-0.09970.682768.341840.039776.6263
23.77961.3915-2.46960.5562-0.85062.2441-0.2353-0.5614-0.4406-0.2171-0.0046-0.1747-0.28650.17740.23991.29410.2142-0.04650.9484-0.07661.250563.411732.225493.2263
31.4816-0.0303-0.27730.41470.25091.1857-0.0235-0.65110.1468-0.05340.0726-0.03870.0752-0.0217-0.04920.5864-0.11620.00761.0584-0.13330.5771.33655.031727.4759
41.7872-0.4709-1.18710.14580.30190.7985-0.0956-0.2639-0.0145-0.08810.0467-0.0410.1370.12940.04890.7624-0.06850.0230.8688-0.02490.69572.6543-1.74099.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A226 - 786
3X-RAY DIFFRACTION1A801 - 802
4X-RAY DIFFRACTION2B19 - 169
5X-RAY DIFFRACTION3C226 - 786
7X-RAY DIFFRACTION3C801 - 802
8X-RAY DIFFRACTION4D19 - 169

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