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Basic information

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


intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding ...intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
Similarity search - Function
MlaA lipoprotein / MlaA lipoprotein / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily ...MlaA lipoprotein / MlaA lipoprotein / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / 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 / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Klebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 31, 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
C: Outer membrane protein F
D: ABC transporter permease
A: Outer membrane protein F
B: ABC transporter permease
E: Outer membrane protein F
F: ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,84623
Polymers190,4366
Non-polymers4,41017
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-262 kcal/mol
Surface area70260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.550, 179.660, 133.390
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules CAEDBF

#1: Protein Outer membrane protein F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein IA / Porin OmpF


Mass: 37114.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#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, SM30_03044, SM57_02930
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8AQT6

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Sugars , 3 types, 3 molecules

#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 940.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][P]{[(0+1)][a-D-AllpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 940.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][P]{[(0+1)][a-D-AllpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+1)][<C8O7>]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 720.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][P]{[(0+1)][a-D-AllpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 14 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, 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: 5.36 Å3/Da / Density % sol: 77.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 3.29→54.27 Å / Num. obs: 60533 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC1/2: 0.98 / Rpim(I) all: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 3.29→3.35 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3023 / CC1/2: 0.743 / Rpim(I) all: 0.534 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFG

2zfg


Resolution: 3.29→47.399 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.16
RfactorNum. reflection% reflection
Rfree0.2591 2950 4.88 %
Rwork0.2193 --
obs0.2212 60457 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.29→47.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 270 0 12920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113232
X-RAY DIFFRACTIONf_angle_d1.30917938
X-RAY DIFFRACTIONf_dihedral_angle_d4.6647453
X-RAY DIFFRACTIONf_chiral_restr0.0711836
X-RAY DIFFRACTIONf_plane_restr0.0082362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.34390.39531230.36482743X-RAY DIFFRACTION99
3.3439-3.40160.39591350.3372743X-RAY DIFFRACTION100
3.4016-3.46340.36081360.31922710X-RAY DIFFRACTION99
3.4634-3.530.29571340.29772742X-RAY DIFFRACTION99
3.53-3.6020.32811610.27562706X-RAY DIFFRACTION99
3.602-3.68030.31671350.27222710X-RAY DIFFRACTION99
3.6803-3.76590.30571490.25722749X-RAY DIFFRACTION99
3.7659-3.86010.30881560.25052711X-RAY DIFFRACTION99
3.8601-3.96440.26531500.24162719X-RAY DIFFRACTION99
3.9644-4.0810.29351300.23612743X-RAY DIFFRACTION99
4.081-4.21260.25651360.22352741X-RAY DIFFRACTION99
4.2126-4.36310.26941550.20492741X-RAY DIFFRACTION100
4.3631-4.53760.2591330.18472729X-RAY DIFFRACTION100
4.5376-4.7440.23151440.192734X-RAY DIFFRACTION99
4.744-4.99380.22571490.19072738X-RAY DIFFRACTION100
4.9938-5.30630.22511420.17772753X-RAY DIFFRACTION99
5.3063-5.71540.26311340.19112756X-RAY DIFFRACTION100
5.7154-6.28940.28051360.18962751X-RAY DIFFRACTION99
6.2894-7.19670.23621680.18422733X-RAY DIFFRACTION100
7.1967-9.05680.21241140.18852792X-RAY DIFFRACTION99
9.0568-47.40390.21571300.23142763X-RAY DIFFRACTION97
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)
11.01880.4972-0.29371.62940.55461.821-0.07-0.04740.02660.24920.0710.0207-0.3627-0.1168-0.0081.00790.1332-0.12751.01350.08281.027533.1955-70.155550.2251
20.0642-0.37760.10683.4127-1.87411.26540.04930.04670.20740.55330.06310.1218-0.54070.0023-0.07861.50530.0453-0.34041.35650.08591.300739.8694-29.792624.4377
30.856-0.27740.07041.2170.31991.8495-0.02790.232-0.1618-0.21950.1402-0.12690.04120.1611-0.07550.8958-0.1609-0.0011.0385-0.0150.906561.8303-73.379425.0312
40.5804-0.2189-0.75362.26380.88761.13220.1207-0.0949-0.0881-0.5210.0039-0.16750.10880.4189-0.1881.8688-0.0568-0.34931.3549-0.2111.247369.9131-112.7104-1.7392
50.8002-0.21570.10941.09990.15510.95750.0611-0.0077-0.37770.17150.08330.25830.3392-0.2318-0.14321.1211-0.1737-0.15440.98680.02761.184845.3767-104.827939.4356
61.65961.7948-1.78123.2424-0.65763.1157-0.0490.4067-0.10740.39880.03360.3210.3716-0.6389-0.03370.7096-0.1984-0.02731.51120.04411.22631.4367-105.97858.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 1 through 340)
2X-RAY DIFFRACTION2(chain 'D' and resid 13 through 211)
3X-RAY DIFFRACTION3(chain 'A' and resid 1 through 340)
4X-RAY DIFFRACTION4(chain 'B' and resid 14 through 211)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 340)
6X-RAY DIFFRACTION6(chain 'F' and resid 14 through 211)

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