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- PDB-4q35: Structure of a membrane protein -

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Basic information

Entry
Database: PDB / ID: 4q35
TitleStructure of a membrane protein
Components(LPS-assembly ...) x 2
KeywordsMEMBRANE PROTEIN / complex / 26 beita-sheet / LPS biogenesis
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Lipoprotein like domain / 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 ...LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Lipoprotein like domain / 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 speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.393 Å
AuthorsHuang, Y. / Qiao, S. / Luo, Q. / Zhao, Y.
CitationJournal: Nature / Year: 2014
Title: Structural basis for lipopolysaccharide insertion in the bacterial outer membrane.
Authors: Qiao, S. / Luo, Q. / Zhao, Y. / Zhang, X.C. / Huang, Y.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,46124
Polymers111,1522
Non-polymers4,30922
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-105 kcal/mol
Surface area44060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.823, 116.620, 68.038
Angle α, β, γ (deg.)90.00, 103.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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LPS-assembly ... , 2 types, 2 molecules AB

#1: Protein LPS-assembly protein LptD


Mass: 91643.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptD, imp, ostA, SF0051, S0053 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q83SQ0
#2: Protein LPS-assembly lipoprotein LptE


Mass: 19509.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptE, rlpB, SF0640, S0662 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83LX4

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Non-polymers , 4 types, 550 molecules

#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.18 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10 mM sodium citrate (pH 5.6), 300mM lithium sulfate, 8% PEG 400, 100mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.393→50 Å / Num. all: 71148 / Num. obs: 71148 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.124
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.59199.6
2.59-3.02199.6
3.02-3.58199.6
3.58-4.1199.6
4.1-5.17199.6
5.17-50199.6

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.393→40.628 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 3666 5.15 %random
Rwork0.1863 ---
obs0.1886 71127 98.74 %-
all-71148 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.393→40.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7307 0 258 528 8093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077805
X-RAY DIFFRACTIONf_angle_d1.25610554
X-RAY DIFFRACTIONf_dihedral_angle_d15.4612946
X-RAY DIFFRACTIONf_chiral_restr0.11077
X-RAY DIFFRACTIONf_plane_restr0.0061369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3928-2.42430.3077980.2388197375
2.4243-2.45750.28431580.2234255899
2.4575-2.49260.27461440.2152619100
2.4926-2.52980.27371530.2106259199
2.5298-2.56930.30121120.20182618100
2.5693-2.61140.25951460.2008261899
2.6114-2.65650.24341270.19432594100
2.6565-2.70470.25511330.1892639100
2.7047-2.75680.24351410.195261599
2.7568-2.8130.26221280.18472609100
2.813-2.87420.25171610.19812588100
2.8742-2.9410.26321350.19722629100
2.941-3.01450.26421470.19932606100
3.0145-3.0960.24841510.19542625100
3.096-3.18710.22161530.1872616100
3.1871-3.28990.23961450.1772599100
3.2899-3.40740.23191130.1832664100
3.4074-3.54380.21251540.17622594100
3.5438-3.7050.19671670.17022602100
3.705-3.90020.24611340.17432643100
3.9002-4.14430.23531310.18192637100
4.1443-4.46390.21381420.16432648100
4.4639-4.91240.17261560.1479257699
4.9124-5.62170.20951530.17852658100
5.6217-7.07660.24941270.20652656100
7.0766-40.63350.19321570.20412686100
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)
10.01850.00990.0080.03380.01030.0013-0.0032-0.00040.02340.00880.06030.0465-0.0172-0.12940.0296-0.16610.0174-0.05530.2655-0.06450.237427.2165-3.7641.9253
20.02030.005-0.00450.07810.05810.05850.05410.0056-0.00680.00680.014-0.01980.03910.0170.08260.1730.04420.0280.01230.00760.045962.048410.78520.0389
30.0942-0.031-0.04640.12160.00450.04650.0612-0.0470.05310.05280.0103-0.04430.03480.04480.07080.07390.0633-0.03070.00210.00890.064361.569437.298420.9814
40.0043-0-0.00280.00130.00070.0011-0.0031-0.0086-0.01530.0027-0.00570.00670.0099-0.024900.11020.03820.0540.1718-0.00540.214537.19336.83730.708
50.0009-0.0005-0.00040.0008-0.00090.0015-0.0022-0.00250.0047-0.0006-0.00330.00810.00040.004-00.10270.00880.05810.17860.02990.141944.32231.60620.532
60.007700.00170.0121-0.01590.02910.0120.0009-0.00150.00290.02040.01750.0131-0.04240.02810.00240.03660.01470.0785-0.00090.0852.70333.30920.992
70.001-0.0023-0.0040.0340.02980.02790.00390.00190.02030.02770.0370.0240.01810.01230.02980.05940.02350.02160.10160.03530.05436.00443.94716.122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 26:231 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 232:387 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 388:784 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 1020:1045 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1046:1072 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1073:1129 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1130:1149 )

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