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- PDB-2w7q: Structure of Pseudomonas aeruginosa LolA -

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Basic information

Entry
Database: PDB / ID: 2w7q
TitleStructure of Pseudomonas aeruginosa LolA
ComponentsOUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN
KeywordsPROTEIN TRANSPORT / PERIPLASMIC CHAPERONE / LIPOPROTEIN TRANSPORT / TRANSPORT / CHAPERONE
Function / homology
Function and homology information


lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta
Similarity search - Domain/homology
Outer-membrane lipoprotein carrier protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRemans, K. / Pauwels, K. / van Ulsen, P. / Savvides, S. / Decanniere, K. / Cornelis, P. / Tommassen, J. / Van Gelder, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Hydrophobic Surface Patches on Lola of Pseudomonas Aeruginosa are Essential for Lipoprotein Binding.
Authors: Remans, K. / Pauwels, K. / Van Ulsen, P. / Buts, L. / Cornelis, P. / Tommassen, J. / Savvides, S. / Decanniere, K. / Van Gelder, P.
History
DepositionDec 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Non-polymer description
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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: OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN
B: OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8564
Polymers45,6722
Non-polymers1842
Water2,666148
1
A: OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0203
Polymers22,8361
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,8361
Polymers22,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.656, 68.439, 61.350
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA35 - 4535 - 45
21THRTHRLEULEUBB35 - 4535 - 45
12ARGARGLEULEUAA51 - 6151 - 61
22ARGARGLEULEUBB51 - 6151 - 61
13ARGARGILEILEAA68 - 8068 - 80
23ARGARGILEILEBB68 - 8068 - 80
14LEULEUASPASPAA88 - 9088 - 90
24LEULEUASPASPBB88 - 9088 - 90
15ILEILELYSLYSAA126 - 129126 - 129
25ILEILELYSLYSBB126 - 129126 - 129
16ASPASPVALVALAA136 - 138136 - 138
26ASPASPVALVALBB136 - 138136 - 138
17THRTHRPHEPHEAA150 - 155150 - 155
27THRTHRPHEPHEBB150 - 155150 - 155
18ASNASNGLNGLNAA161 - 164161 - 164
28ASNASNGLNGLNBB161 - 164161 - 164
19ASNASNPHEPHEAA174 - 178174 - 178
29ASNASNPHEPHEBB174 - 178174 - 178

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Components

#1: Protein OUTER-MEMBRANE LIPOPROTEIN CARRIER PROTEIN / PSEUDOMONAS AERUGINOSA LOLA


Mass: 22835.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / References: UniProt: Q9I0M4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN WAS CLONED WITH N-TERMINAL HISTIDINE TAG AND THROMBINE CLEAVAGE SITE

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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: 1.91 Å3/Da / Density % sol: 35.66 %
Description: CHAINSAW MODEL OF 1UA8 WAS USED FOR MOLECULAR REPLACEMENT
Crystal growpH: 8.5 / Details: 0.1 M TRIS PH 8.5 30% PEG4000 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 1.9→90 Å / Num. obs: 27714 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 11.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UA8

1ua8


Resolution: 1.88→45.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.238 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1380 5 %RANDOM
Rwork0.202 ---
obs0.205 26017 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å2-1.71 Å2
2---1.88 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.88→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 12 148 3046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.9734120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0524.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56715533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0651523
X-RAY DIFFRACTIONr_chiral_restr0.1490.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022291
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22047
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2911.51953
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00623053
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13831206
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8784.51054
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
237medium positional0.20.5
253loose positional0.6515
237medium thermal1.462
253loose thermal2.4525
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 96 -
Rwork0.223 1645 -
obs--85.05 %
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)
10.9941.09310.14831.23450.38251.5066-0.08370.0710.1227-0.378-0.01930.191-0.0240.00640.1030.15190.0504-0.05280.0855-0.00350.12580.45745.76194.6178
22.4585-1.4043-0.11011.92621.60822.4496-0.07890.0941-0.1789-0.1337-0.02540.2513-0.015-0.03790.10430.07760.0156-0.00370.12750.02250.08477.6708-0.7349-3.0032
35.26321.87231.91421.50291.00632.2855-0.0384-0.03020.1949-0.1684-0.08810.36910.0522-0.08080.12650.05090.0366-0.03830.0887-0.04930.1561-4.58154.56088.0369
41.8611-2.3769-0.86023.03871.18442.83210.0367-0.08770.1965-0.13460.2395-0.1938-0.27970.2573-0.27630.07950.00210.0790.2108-0.0170.037415.85182.8207-7.2697
53.3858-1.9641-0.07722.6628-0.323.26550.53060.21220.0261-0.6924-0.3273-0.0632-0.0629-0.0729-0.20340.1620.02720.06890.10810.01860.074612.2058-4.049436.1171
67.50741.1296-1.0665.5353-5.314213.3747-0.09650.03660.10820.11610.2905-0.19180.07590.3023-0.19410.10380.08120.04340.1762-0.01080.01037.92914.178824.8841
73.9243-2.75470.86494.6748-1.41812.18650.2990.3310.4021-0.5868-0.4262-0.66320.08770.2560.12730.11690.02260.12110.12260.06560.098620.3873-4.001238.1808
81.3539-3.26811.37387.8921-3.20095.14550.29390.1274-0.07950.30860.28880.78870.32910.2812-0.58280.1120.0966-0.06470.1263-0.07660.13834.043-1.099122.0657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 67
2X-RAY DIFFRACTION2A68 - 121
3X-RAY DIFFRACTION3A122 - 182
4X-RAY DIFFRACTION4A183 - 204
5X-RAY DIFFRACTION5B20 - 75
6X-RAY DIFFRACTION6B76 - 101
7X-RAY DIFFRACTION7B102 - 183
8X-RAY DIFFRACTION8B184 - 204

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