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- PDB-5uw8: Structure of E. coli MCE protein MlaD, core MCE domain -

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Basic information

Entry
Database: PDB / ID: 5uw8
TitleStructure of E. coli MCE protein MlaD, core MCE domain
DescriptorProbable phospholipid ABC transporter-binding protein MlaD
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Specimen sourceEscherichia coli o157:h7 / bacteria / image: Escherichia coli
MethodX-ray diffraction (2.15 Å resolution / MAD)
AuthorsBhabha, G. / Ekiert, D.C.
CitationCell, 2017, 169, 273-285.e17

Cell, 2017, 169, 273-285.e17 StrPapers
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Ekiert, D.C. / Bhabha, G. / Isom, G.L. / Greenan, G. / Ovchinnikov, S. / Henderson, I.R. / Cox, J.S. / Vale, R.D.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelDatabase references

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Structure visualization

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Assembly

Deposited unit
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
D: Probable phospholipid ABC transporter-binding protein MlaD
E: Probable phospholipid ABC transporter-binding protein MlaD
F: Probable phospholipid ABC transporter-binding protein MlaD
G: Probable phospholipid ABC transporter-binding protein MlaD


Theoretical massNumber of molelcules
Total (without water)94,9497
Polyers94,9497
Non-polymers00
Water2,252125
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)139.660, 103.820, 77.210
Angle α, β, γ (deg.)90.00, 111.03, 90.00
Int Tables number5
Space group name H-MC 1 2 1
DetailsAS PER THE AUTHORS THERE IS SOME AMBIGUITY AS TO WHETHER THIS PROTEIN FORMS A HEPTAMER OR A TETRADECAMER.

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Components

#1: Polypeptide(L)
Probable phospholipid ABC transporter-binding protein MlaD


Mass: 13564.138 Da / Num. of mol.: 7 / Fragment: UNP residues 32-140
Source: (gene. exp.) Escherichia coli o157:h7 / bacteria / image: Escherichia coli
References: UniProt: P64605
#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.75 / Density percent sol: 55.29
Crystal growTemp: 295 K / Method: VAPOR DIFFUSION, SITTING DROP
Details: 0.1 M sodium acetate pH 4.5, and 40% 1,2 propanediol

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Jan 16, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionD resolution high: 2.15 Å / D resolution low: 50 Å / Number obs: 55590 / CC half: 0.46 / NetI over sigmaI: 15.4 / Redundancy: 7.6 / Percent possible obs: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefineMethod to determine structure: MAD / Overall SU ML: 0.34 / Cross valid method: FREE R-VALUE / Sigma F: 0 / Overall phase error: 30.06
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2436 / R factor R work: 0.2039 / R factor obs: 0.2053 / Highest resolution: 2.15 Å / Lowest resolution: 42.12 Å / Number reflection R free: 1810 / Number reflection obs: 49929 / Percent reflection R free: 3.63 / Percent reflection obs: 89.29
Refine hist #LASTHighest resolution: 2.15 Å / Lowest resolution: 42.12 Å
Number of atoms included #LASTProtein: 5502 / Nucleic acid: 0 / Ligand: 0 / Solvent: 125 / Total: 5627
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045703
X-RAY DIFFRACTIONf_angle_d0.9397789
X-RAY DIFFRACTIONf_dihedral_angle_d10.8772114
X-RAY DIFFRACTIONf_chiral_restr0.034935
X-RAY DIFFRACTIONf_plane_restr0.0041016
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.14990.40880.36902.2081113292871.00
2.20810.41750.34332.2730119314276.00
2.27300.35650.31532.3464124324179.00
2.34640.33430.29902.4303125332281.00
2.43030.29920.27642.5276130350084.00
2.52760.32310.25872.6426141363888.00
2.64260.26380.23902.7819139377692.00
2.78190.25980.21822.9561148394295.00
2.95610.22620.21263.1843149400997.00
3.18430.26780.20273.5046155411298.00
3.50460.22560.18914.0114152410699.00
4.01140.20330.15225.05261564173100.00
5.05260.20450.179242.12851594230100.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.7903-0.18060.92452.5936-0.01700.4946-0.08360.1816-0.0652-0.2456-0.0495-0.05880.33750.16790.00010.37180.00240.04720.4944-0.03750.452213.809150.124335.0690
22.8601-2.11031.50781.4759-1.10491.35170.42010.44340.03720.0140-0.33270.03150.0573-0.0521-0.00020.39540.05970.11670.4978-0.02640.332613.672554.035634.8424
32.3213-2.2600-0.10993.4887-1.25241.44840.0684-0.0180-0.3433-0.08210.1962-0.38370.32960.07510.19560.3257-0.02870.10650.4034-0.01410.391315.169447.682140.4038
41.36751.25621.30401.14770.98512.1222-1.0532-0.72211.6300-0.31160.18840.1547-0.6993-1.9450-0.08420.46140.1070-0.02990.5575-0.08320.49665.889155.685541.1567
50.25560.12540.30150.52580.42280.5016-0.71401.36130.9470-1.11271.20510.3817-2.31831.7493-0.03041.38250.25030.02421.22190.03800.88652.808763.784528.8647
63.1558-2.9710-0.41131.9680-0.11160.10301.0206-0.24540.7389-1.25460.36562.2412-1.2762-1.20345.19960.22860.11910.26730.47690.07350.29748.303157.163739.0198
71.10070.33670.00810.3278-0.07840.0348-0.3666-0.0662-1.38020.94960.4340-0.1364-0.15970.54080.00600.71170.08000.04700.62730.03390.528916.999454.471259.0403
80.58160.7845-0.53201.8925-0.31160.5153-0.0990-0.1488-0.81260.49500.02220.28760.2814-0.4847-0.00220.5308-0.00660.03050.6123-0.01070.556113.374747.777545.5107
92.5583-0.13991.74941.56860.57393.38210.64650.9241-1.4496-0.00190.22100.21580.8380-0.11831.31480.53140.1212-0.20650.7740-0.09420.7384-7.306538.898921.7359
100.9797-0.46561.39152.5653-1.66662.5600-0.04810.7850-1.4351-0.36770.8172-0.1653-0.1448-0.51630.51450.75750.0886-0.06920.8889-0.06260.6118-6.762339.073419.0647
111.9113-0.2839-0.08074.2060-2.29551.31081.47640.1788-1.14340.5695-1.4675-0.93650.6213-0.2735-0.13070.56840.1869-0.27990.7997-0.07881.1214-24.694133.651617.5130
129.2020-0.1001-1.63000.6002-1.00412.3866-0.16860.8994-0.1748-0.35800.6114-0.58130.1015-0.05450.39680.61330.0825-0.17740.5932-0.27521.0436-7.986234.793720.4304
134.6681-1.71242.16172.02681.67935.48200.6775-0.7398-1.03100.23230.3451-1.17550.9996-0.41992.57420.5436-0.0274-0.36920.57590.05261.1096-3.994035.391429.9229
140.0012-0.00100.04000.0353-0.06600.0754-0.11083.18221.2753-1.72281.03691.42441.10170.5068-0.00261.16480.0251-0.02010.89410.12471.4103-5.008755.670122.3207
150.63380.2726-0.83530.3351-0.36101.23710.3216-0.1327-0.00680.45370.78131.0533-1.3591-0.28400.10690.53570.0849-0.04920.53970.04680.4849-7.084743.689027.7527
161.85060.04311.98612.48941.03682.58561.1767-1.0866-1.37300.3226-0.05960.11281.0260-1.15450.17400.9513-0.1827-0.43120.74640.10901.0315-9.404731.230531.7196
171.9294-0.24931.65941.8519-0.89901.61110.30400.6377-0.6123-0.1798-0.0671-0.58080.70490.5331-0.06900.53930.0802-0.01960.5154-0.11720.5028-29.738643.66421.9768
183.1656-1.5269-1.09351.9720-0.86861.46830.0680-0.36870.10501.1930-0.2852-0.5256-1.00050.2240-0.14610.4610-0.0706-0.06500.5216-0.04210.5758-25.951354.753910.1648
190.96420.7966-0.29451.40400.80451.60120.23260.0994-0.3294-0.43150.26170.2249-0.7353-0.12690.04460.49370.00990.06330.45240.02520.6433-26.169651.62905.2392
203.95300.51710.30840.2396-0.17162.7094-0.07550.3212-0.5971-0.0061-0.07620.7947-0.6680-0.25600.00310.55390.0770-0.01610.3855-0.08020.2756-35.167454.10973.6669
212.0457-0.89021.74133.1894-3.41135.67810.1316-0.4001-0.43530.6115-0.0658-1.30830.35530.4930-0.03430.47180.0235-0.08350.4970-0.10870.4578-27.320146.348413.4794
220.18250.00240.03919.4847-9.42709.4577-0.03861.7043-0.6480-1.2980-0.71210.34143.33870.3639-0.69990.9628-0.1473-0.11220.6026-0.15620.7901-35.995936.855520.6985
230.2382-0.05840.40840.36990.39291.3603-0.3620-0.12780.7558-1.94550.5092-0.1529-1.2106-0.98030.03280.9175-0.3993-0.08121.2161-0.01421.0204-41.495031.864118.8387
241.6437-1.2586-0.55841.1575-0.40781.89590.1860-0.2302-0.31740.23140.0984-0.05640.4373-1.22140.25760.58830.0150-0.04670.5924-0.02690.3187-36.004246.050210.4972
253.03131.7949-0.04092.61041.94371.59620.26580.53930.4207-1.59090.44520.7887-0.5607-0.63611.17190.95080.0537-0.09050.44420.02470.3757-37.141977.3480-3.0249
260.10290.1438-0.67130.5815-0.30331.52680.21890.2193-0.12390.4220-0.3630-0.6891-0.0597-0.00630.00010.58610.07740.06140.44470.10140.4462-29.887177.87707.7076
270.9971-0.94650.82710.8261-0.3604-0.26650.10160.3747-0.0741-0.0942-0.6245-0.20590.12850.0906-0.00030.69060.06890.12170.48840.06990.4712-33.364085.05294.1580
284.67671.32060.88010.55170.11010.3730-0.44820.54490.2767-1.36190.30841.09520.10620.9931-0.32610.91010.0602-0.02160.51210.08620.3906-34.810779.98450.6284
291.2522-2.6902-0.20879.56691.74810.5666-0.0042-0.0315-1.5054-0.6403-0.56372.82880.8594-0.8913-1.22700.80720.1003-0.16310.4125-0.00060.3279-42.006869.0672-1.1737
306.77933.65711.07622.00180.57260.14731.1900-0.9627-0.87171.2927-0.9081-0.3177-0.01620.35630.07920.87930.02030.04910.46660.10090.4280-33.790774.715212.8918
310.9648-0.13390.02690.0884-0.03890.1077-0.24830.0653-0.36840.05080.0329-1.30620.6483-1.29860.00440.93590.0479-0.02040.88490.08081.0062-20.287371.755213.5005
320.2585-0.1772-0.37960.59740.28990.39440.0851-1.21770.09380.3398-0.5172-0.7188-0.3978-0.1430-0.00120.68120.01740.07090.51750.02360.5379-32.872973.27109.8669
33-0.0081-0.2245-0.10284.05601.71430.72230.7002-0.05560.6765-0.2440-0.64911.65051.8739-1.8823-0.60970.5673-0.1692-0.19301.1157-0.06130.9057-51.792268.61985.5886
340.83370.5692-0.62174.2608-1.26690.60710.44140.16060.29710.4865-0.25250.4213-0.3549-0.0007-0.02680.59360.0734-0.06660.48610.04610.5381-42.182279.18325.5071
352.7439-0.13291.25417.28586.27626.13631.08610.4152-0.4047-1.06740.3307-1.6144-0.61780.53401.32980.6680-0.0439-0.07020.56350.13370.5652-23.6467104.02786.3670
360.7677-0.32901.22461.2894-0.40091.36030.1395-0.1834-0.2625-0.1305-0.3010-0.62370.29030.3075-0.09780.4507-0.0132-0.00220.58880.16950.3951-17.907598.538314.9106
370.78930.32921.20721.88060.85740.9064-0.06210.2001-0.5113-0.41060.3482-0.7626-0.30000.29390.06680.4952-0.0119-0.03370.56270.12260.4748-16.8361108.374118.0622
380.39770.29020.36810.10170.38240.13860.16150.07620.3240-0.4044-0.62370.8494-1.2775-0.6545-0.64170.4725-0.01260.02050.51390.10070.4159-32.8900102.84749.8967
390.4096-0.58541.09642.3446-0.86053.23000.6214-2.5600-1.50430.1166-0.2003-0.39850.49850.47440.51100.6783-0.0919-0.08330.69800.29280.6668-23.348094.579520.7586
406.67563.50073.16666.12317.68951.9692-0.01251.01120.4360-0.95822.3401-0.0516-3.02402.38240.79621.07210.34660.24810.87500.03851.0594-14.503184.465616.4351
410.25230.12580.35361.82070.94351.12130.2744-0.8672-0.8445-0.1228-0.4025-0.36990.46150.6131-0.74030.59940.0495-0.07970.71890.23790.4590-23.362094.465317.4414
424.9662-1.66732.12981.99674.07253.32430.05970.83231.1756-0.57620.8653-0.6355-1.3897-0.53703.74010.63050.21000.17730.51120.33870.6309-42.7971104.358219.1415
431.48570.27781.70250.85051.24594.0084-0.0753-0.85710.31060.5109-0.00190.0225-1.4119-0.1156-0.00800.5148-0.0616-0.03980.55560.04900.6562-27.6473106.388318.0516
443.8588-0.22520.39641.6961-0.11671.3508-0.36350.85070.4533-0.35970.0916-0.33270.17750.5725-0.13480.4620-0.0246-0.06960.61980.12940.54514.6573100.039131.2998
451.12971.9358-0.30604.49030.51590.8590-0.23150.1851-0.2397-0.22000.14360.06840.1196-0.0169-0.00030.4076-0.05500.10420.61960.03360.26181.3858100.424027.2734
460.1850-0.1623-0.19020.12170.14200.1606-0.19840.45250.57921.7076-0.2190-0.8374-1.49690.7905-0.09990.7400-0.0049-0.21090.62600.24420.780813.803698.170243.7055
475.23860.21281.21414.3623-0.50430.7584-1.44420.51801.73720.11190.4606-0.7300-1.04290.1534-0.28090.6759-0.1175-0.18400.66050.19780.8554-0.0288109.200229.8514
483.5233-2.68170.01801.98390.08337.8551-0.6923-0.6067-1.52250.33721.23791.76432.0477-1.87621.57940.5365-0.1167-0.01220.62710.13710.6795-5.508996.040432.7192
492.06091.1215-0.26702.6854-1.02523.8471-0.52820.4665-1.30760.26990.58250.25251.4297-0.0005-0.18080.5553-0.08170.00700.5677-0.02440.6458-5.397494.470528.4538
503.2876-2.8044-0.49852.81171.30451.2175-1.03680.57651.08141.9189-1.3785-1.1964-1.66301.7098-6.05562.13910.1342-0.73460.66600.01051.1851-11.4092117.025939.3565
514.66811.0130-4.84540.2575-0.88126.94190.4038-1.58292.48030.7360-0.91070.1333-1.36771.3004-0.58690.7193-0.0320-0.32560.52310.00751.13102.3300112.239035.8616
521.13600.6030-0.12061.30700.55310.36370.7268-1.4035-0.2790-1.9826-0.10740.17180.2276-2.05330.03850.72360.0495-0.04100.76070.21020.7215-2.964597.773640.1995
531.0108-0.91430.10233.16711.56961.4241-0.21750.2337-0.2273-0.4538-0.03290.2865-0.09660.0968-0.00100.3917-0.07090.02260.39370.05160.502417.420279.326737.1519
542.7119-0.19882.23461.70010.47451.9069-0.32390.01440.27900.42840.1153-0.4393-0.36840.1307-0.01050.3625-0.02380.13630.39630.01590.377020.476979.771444.0132
557.67692.77740.25251.07020.36830.6735-0.6618-0.3804-0.69610.45760.07182.13101.0824-0.8582-0.15100.5149-0.01950.06620.51130.04880.93407.632379.397743.0522
560.4896-0.30110.21360.74740.05260.28660.18390.0394-0.3682-0.0045-0.59061.0987-0.0548-0.8383-0.05240.43940.0336-0.02180.6128-0.06160.76736.371980.462737.1378
577.33042.9964-1.94295.96120.21747.14980.1288-1.5620-0.06430.3992-0.76321.1734-1.00952.1049-1.49710.8142-0.17320.49500.8259-0.06901.127717.238293.145857.0144
581.82610.3205-1.65571.1882-0.96411.9075-0.6069-1.4271-0.47530.36090.10410.51230.52070.1757-0.18740.4158-0.00180.12230.49070.04520.557518.792481.822749.7062
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 109 )
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 115 )
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 62 )
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 73 )
11X-RAY DIFFRACTION11chain 'B' and (resid 74 through 79 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 103 )
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 109 )
15X-RAY DIFFRACTION15chain 'B' and (resid 110 through 115 )
16X-RAY DIFFRACTION16chain 'B' and (resid 116 through 139 )
17X-RAY DIFFRACTION17chain 'C' and (resid 36 through 45 )
18X-RAY DIFFRACTION18chain 'C' and (resid 46 through 62 )
19X-RAY DIFFRACTION19chain 'C' and (resid 63 through 73 )
20X-RAY DIFFRACTION20chain 'C' and (resid 74 through 87 )
21X-RAY DIFFRACTION21chain 'C' and (resid 88 through 115 )
22X-RAY DIFFRACTION22chain 'C' and (resid 116 through 120 )
23X-RAY DIFFRACTION23chain 'C' and (resid 121 through 125 )
24X-RAY DIFFRACTION24chain 'C' and (resid 126 through 140 )
25X-RAY DIFFRACTION25chain 'D' and (resid 37 through 45 )
26X-RAY DIFFRACTION26chain 'D' and (resid 46 through 62 )
27X-RAY DIFFRACTION27chain 'D' and (resid 63 through 79 )
28X-RAY DIFFRACTION28chain 'D' and (resid 80 through 87 )
29X-RAY DIFFRACTION29chain 'D' and (resid 88 through 97 )
30X-RAY DIFFRACTION30chain 'D' and (resid 98 through 103 )
31X-RAY DIFFRACTION31chain 'D' and (resid 104 through 109 )
32X-RAY DIFFRACTION32chain 'D' and (resid 110 through 115 )
33X-RAY DIFFRACTION33chain 'D' and (resid 116 through 127 )
34X-RAY DIFFRACTION34chain 'D' and (resid 128 through 140 )
35X-RAY DIFFRACTION35chain 'E' and (resid 35 through 45 )
36X-RAY DIFFRACTION36chain 'E' and (resid 46 through 73 )
37X-RAY DIFFRACTION37chain 'E' and (resid 74 through 87 )
38X-RAY DIFFRACTION38chain 'E' and (resid 88 through 97 )
39X-RAY DIFFRACTION39chain 'E' and (resid 98 through 103 )
40X-RAY DIFFRACTION40chain 'E' and (resid 104 through 109 )
41X-RAY DIFFRACTION41chain 'E' and (resid 110 through 115 )
42X-RAY DIFFRACTION42chain 'E' and (resid 116 through 125 )
43X-RAY DIFFRACTION43chain 'E' and (resid 126 through 140 )
44X-RAY DIFFRACTION44chain 'F' and (resid 38 through 56 )
45X-RAY DIFFRACTION45chain 'F' and (resid 57 through 73 )
46X-RAY DIFFRACTION46chain 'F' and (resid 74 through 79 )
47X-RAY DIFFRACTION47chain 'F' and (resid 80 through 97 )
48X-RAY DIFFRACTION48chain 'F' and (resid 98 through 104 )
49X-RAY DIFFRACTION49chain 'F' and (resid 105 through 115 )
50X-RAY DIFFRACTION50chain 'F' and (resid 116 through 125 )
51X-RAY DIFFRACTION51chain 'F' and (resid 126 through 135 )
52X-RAY DIFFRACTION52chain 'F' and (resid 136 through 140 )
53X-RAY DIFFRACTION53chain 'G' and (resid 35 through 73 )
54X-RAY DIFFRACTION54chain 'G' and (resid 74 through 97 )
55X-RAY DIFFRACTION55chain 'G' and (resid 98 through 103 )
56X-RAY DIFFRACTION56chain 'G' and (resid 104 through 115 )
57X-RAY DIFFRACTION57chain 'G' and (resid 116 through 123 )
58X-RAY DIFFRACTION58chain 'G' and (resid 124 through 140 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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