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- PDB-5nup: Structural basis for maintenance of bacterial outer membrane lipi... -

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Basic information

Entry
Database: PDB / ID: 5nup
TitleStructural basis for maintenance of bacterial outer membrane lipid asymmetry
Components
  • ABC transporter permease
  • OmpK36
KeywordsMEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / membrane
Similarity search - Function
MlaA lipoprotein / MlaA lipoprotein / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin ...MlaA lipoprotein / MlaA lipoprotein / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lipoprotein / OmpK36 / OmpC protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAbellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union115525 United Kingdom
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural basis for maintenance of bacterial outer membrane lipid asymmetry.
Authors: Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.
History
DepositionMay 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpK36
B: OmpK36
C: OmpK36
D: ABC transporter permease
E: ABC transporter permease
F: ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,54128
Polymers193,1866
Non-polymers7,35422
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26080 Å2
ΔGint-55 kcal/mol
Surface area69010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.377, 145.240, 232.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OmpK36


Mass: 38030.934 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QLY0, UniProt: F2VN85*PLUS
#2: Protein ABC transporter permease / Lipoprotein / Phospholipid-binding lipoprotein MlaA / Putative phospholipid-binding lipoprotein ...Lipoprotein / Phospholipid-binding lipoprotein MlaA / Putative phospholipid-binding lipoprotein MlaA / VacJ protein


Mass: 26364.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: mlaA, vacJ, AGG09_21815, BB749_07690, BCB67_11070, BL143_09030, BN49_3944, PMK1_00224, SAMEA3531778_01593, SM57_02930
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8AQT6
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.04 M magnesium chloride hexahydrate, 0.05 M sodium chloride, 0.1 M HEPES pH7.5 and 32 % PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→145.2 Å / Num. obs: 70200 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rpim(I) all: 0.068 / Net I/σ(I): 7
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4460 / CC1/2: 0.82 / Rpim(I) all: 0.408 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX(1.11.1_2575: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OSM

1osm


Resolution: 2.9→68.383 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5
RfactorNum. reflection% reflection
Rfree0.2905 3408 4.87 %
Rwork0.2408 --
obs0.2432 70035 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→68.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12893 0 345 0 13238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113550
X-RAY DIFFRACTIONf_angle_d1.36818281
X-RAY DIFFRACTIONf_dihedral_angle_d11.7997762
X-RAY DIFFRACTIONf_chiral_restr0.0721848
X-RAY DIFFRACTIONf_plane_restr0.0092399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.94140.42421330.34422711X-RAY DIFFRACTION100
2.9414-2.98540.36981540.33152738X-RAY DIFFRACTION100
2.9854-3.0320.40311500.31072724X-RAY DIFFRACTION100
3.032-3.08170.39121490.30212762X-RAY DIFFRACTION100
3.0817-3.13490.34711130.28562731X-RAY DIFFRACTION100
3.1349-3.19190.33241580.26972741X-RAY DIFFRACTION100
3.1919-3.25320.32821580.26712725X-RAY DIFFRACTION100
3.2532-3.31970.32531350.26312753X-RAY DIFFRACTION100
3.3197-3.39180.32721290.26192756X-RAY DIFFRACTION100
3.3918-3.47070.33481370.26042759X-RAY DIFFRACTION100
3.4707-3.55750.34621190.24822789X-RAY DIFFRACTION100
3.5575-3.65370.30711350.2382745X-RAY DIFFRACTION100
3.6537-3.76120.28811440.23222751X-RAY DIFFRACTION100
3.7612-3.88260.28661500.22712747X-RAY DIFFRACTION100
3.8826-4.02140.30791410.22752793X-RAY DIFFRACTION100
4.0214-4.18230.28911410.22962771X-RAY DIFFRACTION100
4.1823-4.37270.28031440.22062764X-RAY DIFFRACTION100
4.3727-4.60310.25851470.20162788X-RAY DIFFRACTION100
4.6031-4.89150.25261550.19922783X-RAY DIFFRACTION100
4.8915-5.2690.24821350.20722795X-RAY DIFFRACTION100
5.269-5.7990.24461430.22172827X-RAY DIFFRACTION100
5.799-6.63750.24431590.22482818X-RAY DIFFRACTION100
6.6375-8.36020.26771500.23532859X-RAY DIFFRACTION100
8.3602-68.40180.27241290.27022997X-RAY DIFFRACTION99
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)
10.5848-0.2978-0.05570.91960.0711.1671-0.03990.0448-0.10860.07390.0205-0.05310.2003-0.0810.01750.9521-0.054-0.00320.3917-0.00450.4928-16.218432.6211-59.4688
20.73880.14010.11361.054-0.4471.3747-0.07310.03830.13820.20230.0488-0.046-0.3885-0.08860.01630.98910.0198-0.01670.4203-0.00920.4912-17.349770.1265-67.4819
30.87890.0602-0.29311.76630.26781.1554-0.08560.2540.0095-0.39080.1066-0.2226-0.17050.0024-0.01531.0628-0.07770.05070.5589-0.01620.4578-10.11444.7227-95.3659
41.2772-0.7472-1.19880.85950.98851.9482-0.03-0.1330.29330.49650.13680.1094-0.5058-0.2509-0.11911.12660.18620.05970.4962-0.00370.5081-38.464160.515-25.7606
51.16971.74190.59443.92021.19531.1268-0.00070.0423-0.3750.05310.0496-0.31430.1576-0.0159-0.05250.9603-0.04580.04770.4858-0.06650.6234-23.9768-2.4905-91.7454
60.65-0.2079-0.4662.4501-1.6271.63580.13230.25520.14140.06540.1890.2166-0.7222-0.6494-0.29711.18250.18090.04090.73990.12570.5375-25.980686.9536-112.82
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 342)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 342)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 342)
4X-RAY DIFFRACTION4(chain 'D' and resid 13 through 211)
5X-RAY DIFFRACTION5(chain 'E' and resid 13 through 211)
6X-RAY DIFFRACTION6(chain 'F' and resid 13 through 216)

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