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- PDB-5c76: ATP-driven lipid-linked oligosaccharide flippase PglK in apo-inwa... -

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Basic information

Entry
Database: PDB / ID: 5c76
TitleATP-driven lipid-linked oligosaccharide flippase PglK in apo-inward facing state (2)
ComponentsWlaB protein
KeywordsTRANSPORT PROTEIN / ABC transporter flippase
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.94 Å
AuthorsPerez, C. / Gerber, S. / Locher, K.P.
CitationJournal: Nature / Year: 2015
Title: Structure and mechanism of an active lipid-linked oligosaccharide flippase.
Authors: Perez, C. / Gerber, S. / Boilevin, J. / Bucher, M. / Darbre, T. / Aebi, M. / Reymond, J.L. / Locher, K.P.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WlaB protein
B: WlaB protein
C: WlaB protein
D: WlaB protein


Theoretical massNumber of molelcules
Total (without water)258,3514
Polymers258,3514
Non-polymers00
Water0
1
A: WlaB protein
D: WlaB protein


Theoretical massNumber of molelcules
Total (without water)129,1752
Polymers129,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-101 kcal/mol
Surface area55670 Å2
MethodPISA
2
B: WlaB protein
C: WlaB protein


Theoretical massNumber of molelcules
Total (without water)129,1752
Polymers129,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-100 kcal/mol
Surface area55620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.410, 183.330, 136.260
Angle α, β, γ (deg.)90.000, 106.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 564 / Label seq-ID: 1 - 564

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
WlaB protein /


Mass: 64587.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaB / Production host: Escherichia coli bl21(de3) (bacteria) / References: UniProt: O86150

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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: 4.33 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.4 / Details: Glycine-NaOH; KCl; MgCl2; PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.94→30 Å / Num. obs: 33489 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 166.27 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.097 / Χ2: 0.93 / Net I/σ(I): 12.36 / Num. measured all: 480068
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.94-4.040.6672.0361.54282528912922.1510.1
4.04-4.150.6891.8781.61974327968651.96730.9
4.15-4.270.7742.0241.5525511272319282.10670.8
4.27-4.40.8581.4322.0736627261726111.48699.8
4.4-4.550.9290.9543.2739189256425660.987100
4.55-4.710.9720.624.8638025248624820.64199.8
4.71-4.890.9830.4596.4836324238623840.47499.9
4.89-5.090.9910.3358.4934693229722940.34699.9
5.09-5.310.9910.328.8633594221722160.331100
5.31-5.570.9860.3468.5631860211921120.35899.7
5.57-5.870.9830.3279.1429938201720130.33899.8
5.87-6.230.9880.2611.1427961192019190.26999.9
6.23-6.660.9920.18914.5225200176217630.196100
6.66-7.190.9960.13119.2722892167716720.13699.7
7.19-7.880.9970.09224.8619039153715370.096100
7.88-8.810.9980.06730.9817485137913780.0799.9
8.81-10.170.9990.05936.4617325123012310.061100
10.17-12.460.9990.05139.1315149105310470.05399.4
12.46-17.620.9990.04939.23116318158150.051100
17.620.9990.04239.5250574623640.04378.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.39 Å29.82 Å
Translation4.39 Å29.82 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C78

5c78


Resolution: 3.94→29.823 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 41.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3293 1692 5.05 %
Rwork0.2745 31782 -
obs0.2773 33474 86.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 371.52 Å2 / Biso mean: 208.3747 Å2 / Biso min: 111.4 Å2
Refinement stepCycle: final / Resolution: 3.94→29.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18228 0 0 0 18228
Num. residues----2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418564
X-RAY DIFFRACTIONf_angle_d0.93924984
X-RAY DIFFRACTIONf_chiral_restr0.0352896
X-RAY DIFFRACTIONf_plane_restr0.0043084
X-RAY DIFFRACTIONf_dihedral_angle_d15.4136916
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10813X-RAY DIFFRACTION8.899TORSIONAL
12B10813X-RAY DIFFRACTION8.899TORSIONAL
13C10813X-RAY DIFFRACTION8.899TORSIONAL
14D10813X-RAY DIFFRACTION8.899TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9395-4.05520.3715150.415835336811
4.0552-4.18580.394570.36521093115036
4.1858-4.33490.38711500.35742664281487
4.3349-4.50790.36591590.33830683227100
4.5079-4.71230.38371610.315230823243100
4.7123-4.95970.36681680.285730463214100
4.9597-5.26890.30071540.288930733227100
5.2689-5.67310.35961620.322930743236100
5.6731-6.23930.40411590.332130873246100
6.2393-7.13130.34621490.311330783227100
7.1313-8.94430.27451850.251530583243100
8.9443-29.82360.3061730.217931063279100
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)
11.20141.5344-0.12272.04740.17052.2151-0.0913-0.66040.91050.67970.1281-2.3564-0.33830.11820.28041.0701-0.0205-0.34410.9212-0.11862.572241.613545.178719.2463
21.09920.198-0.05942.21770.29760.08440.3884-0.55950.84542.0591-0.5621-1.0691-0.2923-0.3942-1.16121.371-0.04490.41091.374-0.47180.987710.233431.686727.7013
33.80153.2769-2.84897.0958-0.30383.04731.056-0.89421.06671.70650.3866-0.864-0.56641.71640.60091.4035-0.16990.23281.1439-0.39931.875121.214857.389526.955
43.3607-0.42470.46094.1137-0.48622.9414-0.5413-0.2357-0.17420.78890.1533-0.5463-0.06560.15110.15091.35060.0999-0.35820.5095-0.11491.03531.0486-12.638219.9748
50.9572-0.9262-0.95532.01320.34631.55240.9533-1.14361.5235-0.2777-0.7581.5985-0.362-0.599-1.67730.40910.20690.48923.2885-1.70472.6596-17.507316.485683.8391
60.08760.01970.5470.67371.28612.3672-0.2009-0.31720.80750.0847-0.01940.5045-0.31250.20610.20781.2161-0.220.04071.2126-0.26931.821813.673817.164671.0577
70.3815-1.0425-0.27114.34071.64792.93610.89360.44310.0867-0.81531.8672-0.7269-1.24860.62960.98181.3634-0.04130.14222.3186-0.96082.4045-2.882730.602484.8946
84.39680.0135-0.13093.2141-0.52921.9796-0.29940.4027-1.13990.5263-0.67981.38860.7171-1.12160.951.6766-0.14580.09241.4845-0.61151.8827-3.0991-24.624643.7123
94.416-0.5411-0.57440.9346-1.28053.3797-0.4015-1.0899-0.16041.3014-0.33830.1083-0.26921.80060.15081.0982-0.3080.21561.31230.00661.138224.738320.665493.4453
101.6212.89672.56233.19553.64123.1651-0.49581.1729-0.2414-0.02980.66010.5575-0.22242.1055-0.32011.848-0.19570.09751.5767-0.37411.1903-4.1669-1.164779.809
112.088-0.9809-1.65332.4996-0.7942.6082-0.3620.09160.2268-0.5755-0.73861.23640.4466-1.7957-0.01971.43070.1017-0.03953.012-1.14782.84434.452719.5998100.9657
123.0262-1.20011.5935.98270.9081.8621-0.67181.2786-1.6952-0.0721-0.15670.79310.76260.71070.29431.75760.63250.3513.186-0.00262.197553.1025-7.234758.774
133.5359-0.7015-1.65734.9745-0.8915.2585-0.56430.84040.2483-0.3711-0.01133.4415-0.8029-1.90030.06921.38741.0258-0.799-0.15410.23152.64812.992665.545814.7901
145.67020.9493-1.68580.79-1.08681.5298-0.9860.8056-0.0853-0.30480.51330.57410.2166-0.74320.35071.3557-0.073-0.15211.48610.12831.5142-4.285941.865912.629
15-0.0872-0.15310.04553.9641-3.312.0639-0.62710.18230.1869-3.03651.32940.53081.1781-0.4761-0.36231.70990.1288-0.38091.04260.55991.552529.585723.97299.7827
160.12180.47140.12666.1311-1.88971.72360.3673-0.37911.71370.1674-0.16861.53930.3962-0.9584-0.20011.6179-0.02850.21591.03420.06812.620922.674555.5718.553
171.6004-1.192-0.15672.6084-1.14440.5571-1.05890.1388-0.9977-0.42590.8943-0.043-0.1158-1.37750.26161.7679-0.70120.13611.9252-0.37812.1117-26.49145.350117.1913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 255 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 316 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 564 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 118 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 275 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 276 through 319 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 320 through 564 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 170 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 171 through 275 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 276 through 318 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 319 through 564 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 72 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 73 through 170 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 171 through 255 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 256 through 318 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 319 through 564 )D0

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