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- PDB-5c78: ATP-driven lipid-linked oligosaccharide flippase PglK in apo-inwa... -

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Basic information

Entry
Database: PDB / ID: 5c78
TitleATP-driven lipid-linked oligosaccharide flippase PglK in apo-inward state (1)
ComponentsATP-driven flippase PglK
KeywordsHYDROLASE / 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 / MIR / molecular replacement / Resolution: 2.9 Å
AuthorsPerez, C. / 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 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: ATP-driven flippase PglK
B: ATP-driven flippase PglK
C: ATP-driven flippase PglK
D: ATP-driven flippase PglK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,5429
Polymers258,3514
Non-polymers1,1915
Water2,072115
1
A: ATP-driven flippase PglK
D: ATP-driven flippase PglK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6524
Polymers129,1752
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-95 kcal/mol
Surface area52760 Å2
MethodPISA
2
B: ATP-driven flippase PglK
C: ATP-driven flippase PglK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8905
Polymers129,1752
Non-polymers7153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-100 kcal/mol
Surface area52830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.600, 114.420, 145.590
Angle α, β, γ (deg.)68.440, 73.270, 68.670
Int Tables number1
Space group name H-MP1
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
ATP-driven flippase PglK


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
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 5.31 Å3/Da / Density % sol: 76.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.2 / Details: Tris-HCl; MgAcetate; PEG400

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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: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 206754 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 71.64 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.117 / Χ2: 1.012 / Net I/σ(I): 8.9 / Num. measured all: 1176105
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
2.9-2.970.4861.2021.3469541897412031.32223
2.89-2.970.571.1881.31241501873643101.30923
2.97-3.050.5731.5681.06524671801487251.71448.4
3.05-3.150.691.3661.247128617566117811.49267.1
3.15-3.250.7431.2151.398463617144142041.32982.9
3.25-3.360.8470.9161.819361716474159331.00496.7
3.36-3.490.9320.6042.69220315920158830.66399.8
3.49-3.630.9670.3813.878899715392153530.41899.7
3.63-3.790.9790.2675.348221714578145490.29499.8
3.79-3.980.9850.1937.027516613970139450.21499.8
3.98-4.20.990.1419.167073713398133670.15799.8
4.2-4.450.9910.111126692212598125700.12399.8
4.45-4.760.9950.09215.146908511874118260.10199.6
4.76-5.140.9950.08416.556400511036110040.09399.7
5.14-5.630.9950.08716.715849910164101170.09599.5
5.63-6.290.9940.08417.5251672918091520.09299.7
6.29-7.270.9940.07319.3642770807279990.08199.1
7.27-8.90.9960.05622.5634946687268450.06299.6
8.9-12.590.9970.05126.3430108528852450.05699.2
12.590.9960.05326.7215668289027430.05994.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.9→27.928 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 5133 5 %
Rwork0.2315 97460 -
obs0.2333 102593 87.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.07 Å2 / Biso mean: 80.7514 Å2 / Biso min: 23.06 Å2
Refinement stepCycle: final / Resolution: 2.9→27.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18228 0 80 115 18423
Biso mean--69.55 45.12 -
Num. residues----2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118804
X-RAY DIFFRACTIONf_angle_d1.58625208
X-RAY DIFFRACTIONf_chiral_restr0.0652896
X-RAY DIFFRACTIONf_plane_restr0.0073084
X-RAY DIFFRACTIONf_dihedral_angle_d20.0287124
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10677X-RAY DIFFRACTION10.59TORSIONAL
12B10677X-RAY DIFFRACTION10.59TORSIONAL
13C10677X-RAY DIFFRACTION10.59TORSIONAL
14D10677X-RAY DIFFRACTION10.59TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.93290.397600.393772678620
2.9329-2.96740.3623520.39811102115430
2.9674-3.00350.4366960.38321620171643
3.0035-3.04150.398970.39011909200652
3.0415-3.08150.38691280.36842264239261
3.0815-3.12370.37111280.36832537266568
3.1237-3.16820.37571460.3682811295775
3.1682-3.21540.38561680.3743078324683
3.2154-3.26560.37681700.34713311348189
3.2656-3.31910.3831800.33973609378997
3.3191-3.37620.38491790.334437423921100
3.3762-3.43750.33441930.309237393932100
3.4375-3.50350.35112020.291136833885100
3.5035-3.57490.32621880.267837833971100
3.5749-3.65240.31062020.252536483850100
3.6524-3.73720.27421940.245337873981100
3.7372-3.83040.26832050.233336943899100
3.8304-3.93370.25861970.227337423939100
3.9337-4.04910.24791990.226537233922100
4.0491-4.17940.25911890.219437243913100
4.1794-4.32830.27062060.197336923898100
4.3283-4.50090.19921930.18537533946100
4.5009-4.70480.21281910.173737133904100
4.7048-4.95160.21571900.170237413931100
4.9516-5.25990.20412200.173437013921100
5.2599-5.66290.27241900.202437453935100
5.6629-6.2270.25171960.208137023898100
6.227-7.11510.23251980.199437573955100
7.1151-8.91560.21531900.183937173907100
8.9156-27.92940.24141860.21883707389399
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)
10.92840.41080.16210.8796-0.5190.89530.2074-0.2086-0.15940.1046-0.10720.0204-0.1113-0.087-0.04950.51320.09060.09220.3918-0.11570.2737121.3733106.7198102.5656
22.7889-1.2682.69421.1124-1.66323.3754-0.4176-0.1399-0.18560.27310.22640.214-0.0884-0.09150.15410.69660.11790.23550.79150.10440.4121109.8172110.063899.5322
33.6257-1.1878-0.50173.1357-1.0733.65680.04910.52930.3832-0.6041-0.1719-0.41370.89450.16290.06050.44030.03780.06190.54490.15040.5133100.9987131.505254.9906
41.41270.8053-0.71684.6504-2.14722.59790.07630.48440.5690.02560.32570.3709-0.4833-0.75-0.0850.52650.0752-0.04860.50230.07480.497114.6528109.760818.7966
50.2266-0.55230.07340.9591-0.17150.01060.09310.09150.1342-0.4269-0.0731-0.00940.3124-0.0024-0.01380.70140.0444-0.09080.6891-0.02130.3389139.844588.009410.8781
62.87251.5408-2.98532.4924-2.21923.6465-0.56810.1436-0.1082-0.71240.0195-0.28240.15770.00940.46980.8371-0.235-0.21450.87870.08090.5049116.350994.852317.306
74.2011.78930.42363.6246-1.06332.69810.165-0.5851-0.30270.5274-0.2031-0.1957-0.55970.06490.07480.3778-0.02540.0130.51780.07350.3923107.493571.356560.614
82.3736-1.2830.85113.0157-1.78462.740.13580.96720.9066-0.1183-0.5395-0.9741-0.21910.6190.15140.5418-0.15770.02250.56590.09210.5747157.8726101.57735.1503
90.26260.0122-0.3920.4267-0.44120.8060.1478-0.07410.06390.1979-0.0741-0.1625-0.24910.0969-0.11720.6216-0.1715-0.08730.3655-0.04310.4195133.6029102.619329.08
103.8066-0.9138-1.10043.0881.73941.55210.0641-0.06760.3387-0.67560.58850.54480.1328-0.6816-0.37650.9784-0.276-0.48760.76280.37611.3181145.2879113.328812.9871
112.54230.57930.70242.991-0.87912.4648-0.01260.0776-0.5661-0.8019-0.0603-0.24670.25580.13140.02390.3370.07660.15940.5603-0.00920.6732169.484454.609531.156
123.44471.3546-0.69311.7417-0.06530.42550.3437-1.0166-1.12050.5913-0.4735-0.7354-0.00380.3899-0.24290.57170.0086-0.04230.4191-0.06790.3911151.4341103.487112.2277
131.0028-0.06270.84660.2417-0.32110.93050.29740.1415-0.026-0.1936-0.0855-0.08270.23610.0666-0.19490.63590.09630.05880.3407-0.08620.4576127.0841102.227287.8691
142.4421.1774-0.14253.45312.40312.13130.4043-0.2636-0.390.1470.42060.45120.3081-0.6978-0.55390.74060.03090.12270.82410.59631.5065138.009490.3804105.2496
153.0126-0.5209-0.47931.77420.08312.4127-0.03140.0168-0.07530.3861-0.2882-0.43550.01640.25720.14980.2607-0.0616-0.11040.58070.11950.6562168.5964142.212579.1532
163.7092-0.2557-2.01053.4396-1.30727.0292-0.00430.10850.79330.93060.2489-0.087-0.4887-0.1342-0.27120.5973-0.0495-0.08290.33530.01010.6967158.0751155.920389.0527
170.06590.0991-0.04830.2027-0.20680.1438-0.09150.00430.0301-0.0281-0.0363-0.09210.0972-0.0388-0.0220.5237-0.00110.02960.54-0.37330.4289132.4576102.564956.995
18-0.0398-0.03310.0077-0.04990.0352-0.013-0.00920.04690.03950.0298-0.0131-0.0845-0.04640.0214-0.21210.19260.14330.08430.3041-0.39610.2186134.7537103.376661.5406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 277 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 278 through 347 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 348 through 564 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 128 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 129 through 277 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 278 through 347 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 348 through 564 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 128 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 129 through 280 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 281 through 319 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 320 through 564 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 128 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 129 through 277 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 278 through 319 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 320 through 438 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 439 through 564 )D0
17X-RAY DIFFRACTION17chain 'E'E1265 - 1269
18X-RAY DIFFRACTION18chain 'F'F2 - 116

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