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- PDB-5udf: Structure of the N-terminal domain of lipoprotein-releasing syste... -

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Basic information

Entry
Database: PDB / ID: 5udf
TitleStructure of the N-terminal domain of lipoprotein-releasing system transmembrane protein LolE from Acinetobacter baumannii
ComponentsLipoprotein-releasing system transmembrane protein LolE
KeywordsPROTEIN TRANSPORT / SSGCID / Acinetobacter baumannii / Lipoprotein-releasing system / LolE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyLipoprotein-releasing system transmembrane protein LolC/E / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC3 transporter permease protein domain / FtsX-like permease family / lipoprotein transport / membrane => GO:0016020 / plasma membrane / ABC-type transport system
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of the N-terminal domain of lipoprotein-releasing system transmembrane protein LolE from Acinetobacter baumannii
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: Lipoprotein-releasing system transmembrane protein LolE
B: Lipoprotein-releasing system transmembrane protein LolE
C: Lipoprotein-releasing system transmembrane protein LolE
D: Lipoprotein-releasing system transmembrane protein LolE


Theoretical massNumber of molelcules
Total (without water)100,6634
Polymers100,6634
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-75 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.370, 156.370, 91.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 67 through 70 and (name N...
21(chain B and ((resid 67 through 70 and (name N...
31(chain C and ((resid 67 through 70 and (name N...
41(chain D and ((resid 67 through 70 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEU(chain A and ((resid 67 through 70 and (name N...AA67 - 7013 - 16
12ASNASN(chain A and ((resid 67 through 70 and (name N...AA67 - 27713 - 223
13ASNASN(chain A and ((resid 67 through 70 and (name N...AA67 - 27713 - 223
14ASNASN(chain A and ((resid 67 through 70 and (name N...AA67 - 27713 - 223
15ASNASN(chain A and ((resid 67 through 70 and (name N...AA67 - 27713 - 223
21LEULEU(chain B and ((resid 67 through 70 and (name N...BB67 - 7013 - 16
22PHEPHE(chain B and ((resid 67 through 70 and (name N...BB67 - 27613 - 222
23PHEPHE(chain B and ((resid 67 through 70 and (name N...BB67 - 27613 - 222
24PHEPHE(chain B and ((resid 67 through 70 and (name N...BB67 - 27613 - 222
25PHEPHE(chain B and ((resid 67 through 70 and (name N...BB67 - 27613 - 222
31LEULEU(chain C and ((resid 67 through 70 and (name N...CC67 - 7013 - 16
32THRTHR(chain C and ((resid 67 through 70 and (name N...CC67 - 27113 - 217
33THRTHR(chain C and ((resid 67 through 70 and (name N...CC67 - 27113 - 217
34THRTHR(chain C and ((resid 67 through 70 and (name N...CC67 - 27113 - 217
35THRTHR(chain C and ((resid 67 through 70 and (name N...CC67 - 27113 - 217
41LEULEU(chain D and ((resid 67 through 70 and (name N...DD67 - 7013 - 16
42THRTHR(chain D and ((resid 67 through 70 and (name N...DD67 - 27113 - 217
43THRTHR(chain D and ((resid 67 through 70 and (name N...DD67 - 27113 - 217
44THRTHR(chain D and ((resid 67 through 70 and (name N...DD67 - 27113 - 217
45THRTHR(chain D and ((resid 67 through 70 and (name N...DD67 - 27113 - 217

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Components

#1: Protein
Lipoprotein-releasing system transmembrane protein LolE


Mass: 25165.861 Da / Num. of mol.: 4 / Fragment: AcbaC.18885.a.B2 / Mutation: UNP residues 63-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: lolC, lolE, ABUW_0974, LV38_03997 / Plasmid: AcbaC.18885.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5YFP2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Native data set: Microlytic MCSG1 screen H6: 3.5M Sodium formate, 100mM Sodium Acetate / HCl pH 4.6: AcbaC.18885.a.B2.PS02462 at 14.5mg/ml, cryo: 20% EG, tray 265717h6, puck xck3-10. SeMet ...Details: Native data set: Microlytic MCSG1 screen H6: 3.5M Sodium formate, 100mM Sodium Acetate / HCl pH 4.6: AcbaC.18885.a.B2.PS02462 at 14.5mg/ml, cryo: 20% EG, tray 265717h6, puck xck3-10. SeMet data set: Microlytic MCSG1 screen H6 optimization: 3M Sodium formate, 100mM Sodium Acetate / HCl pH 4.43: AcbaC.18885.a.B2.PS38034 at 18.0mg/ml, cryo: well D12: 4M Sodium formate, 100mM Sodium Acetate/HCl pH 4.43: tray 265717h6, puck xck3-10

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
SYNCHROTRONAPS 21-ID-G20.97856
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDAug 21, 2016
RAYONIX MX-3002CCDDec 16, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2Diamond [111]SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
20.978561
ReflectionResolution: 2.35→45.14 Å / Num. obs: 34401 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.733 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsCC1/2% possible all
2.35-2.413.0230.4992.2924280.70494.7
2.41-2.483.6370.4393.010.79699.5
2.48-2.553.9010.3593.770.86599.9
2.55-2.633.9020.294.60.90999.8
2.63-2.713.910.2315.860.93100
2.71-2.813.90.1787.310.96499.9
2.81-2.913.880.1359.630.976100
2.91-3.033.8650.10711.930.983100
3.03-3.173.8370.08914.250.98899.9
3.17-3.323.7770.06917.540.99399.9
3.32-3.53.7150.05820.20.99599.8
3.5-3.723.7360.04823.160.99699.7
3.72-3.973.7290.04424.930.99699.8
3.97-4.293.7480.0427.090.99798.9
4.29-4.73.6620.03928.870.99699.2
4.7-5.253.660.03929.120.99699.1
5.25-6.073.6030.04128.890.99699.6
6.07-7.433.6640.03829.770.99699.5
7.43-10.513.7340.03231.470.99799.6
10.51-503.5280.03330.90.99898.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building
PHENIXdev_2621refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.35→45 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.32
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 2095 6.09 %0
Rwork0.1764 ---
obs0.179 34397 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.52 Å2 / Biso mean: 50.8222 Å2 / Biso min: 21.97 Å2
Refinement stepCycle: final / Resolution: 2.35→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 0 117 6092
Biso mean---44.66 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066114
X-RAY DIFFRACTIONf_angle_d0.828366
X-RAY DIFFRACTIONf_chiral_restr0.0541021
X-RAY DIFFRACTIONf_plane_restr0.0061078
X-RAY DIFFRACTIONf_dihedral_angle_d10.9633633
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3257X-RAY DIFFRACTION6.741TORSIONAL
12B3257X-RAY DIFFRACTION6.741TORSIONAL
13C3257X-RAY DIFFRACTION6.741TORSIONAL
14D3257X-RAY DIFFRACTION6.741TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40470.31651340.24742069220394
2.4047-2.46480.2881330.23692132226599
2.4648-2.53140.29081740.234921432317100
2.5314-2.60590.27451360.226121512287100
2.6059-2.690.28341110.216521922303100
2.69-2.78620.25231220.21422152337100
2.7862-2.89770.27521540.211421362290100
2.8977-3.02960.26961780.197421252303100
3.0296-3.18920.24931680.191421522320100
3.1892-3.3890.21411110.181122042315100
3.389-3.65050.22511070.170821682275100
3.6505-4.01770.21331410.157421632304100
4.0177-4.59860.16071650.14722121228699
4.5986-5.79180.17351190.15552167228699
5.7918-45.14840.20131420.15842164230699
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)
13.9356-0.0768-0.57864.8312-1.17442.50270.04510.7299-0.1695-0.7466-0.0570.10030.2481-0.40720.04220.3959-0.0684-0.03490.5786-0.02250.3012-11.802731.679513.8897
22.38810.2465-1.49474.4717-1.33573.69890.03490.2606-0.18470.00520.00150.2538-0.22940.3295-0.01660.2645-0.0334-0.01090.3414-0.03110.3005-15.983730.973926.611
33.24150.1518-0.65914.4303-1.35872.4317-0.1049-0.1044-0.40250.44290.18310.59520.0304-0.2416-0.06520.3513-0.03760.08680.3157-0.02380.3712-22.331925.853232.7205
45.0803-0.4743-4.89992.5816-0.55935.1562-0.57820.2702-0.48640.8743-0.59811.48970.0341-0.30531.03140.6918-0.16640.10240.486-0.10770.7904-10.393348.919140.8544
52.44771.1397-0.3315.0111-0.54183.42840.06310.07250.02780.1713-0.02750.155-0.01640.2825-0.02590.2356-0.05-0.0260.3409-0.04860.3116-17.415232.371626.8604
64.5651-0.90331.11465.63570.53431.2623-0.12510.27760.5124-0.1363-0.2678-0.8907-0.03520.29410.35930.3709-0.08050.04780.44190.07680.4717-1.924436.836815.042
73.92271.34320.55212.2690.72312.5619-0.1450.1826-0.63160.22320.0268-0.30140.28050.0554-0.03680.3834-0.02270.0270.35910.00770.45312.254621.754927.4096
82.90481.7361-0.73482.3272-0.97842.24440.0006-0.10590.0154-0.48130.29380.13090.05190.15-0.13510.32090.0439-0.05650.2626-0.05570.283314.136633.919425.8207
92.3248-1.8805-0.14719.4485-0.27163.5194-0.13190.46-0.22530.2635-0.1353-0.27410.28210.060.22010.308-0.02920.05620.3923-0.04130.338117.487534.066421.2268
104.7880.86180.10564.22650.75313.6011-0.20720.20690.5514-0.13640.1273-0.6469-0.2345-0.07120.01860.3717-0.06410.03110.3936-0.0570.474321.755739.870118.0008
117.03020.3176-2.3228.84382.06257.5168-0.0722-0.03440.1557-0.09870.0718-0.0846-0.9037-0.51960.19490.31890.0092-0.01560.35090.01710.309819.532341.374618.8478
123.58051.70130.13564.93960.15343.9530.11250.1532-0.04430.3123-0.128-0.1073-0.0216-0.2854-0.0320.33170.0567-0.01730.2854-0.05260.333516.236231.784927.5957
138.53862.33960.9446.2738-0.31921.71410.4697-0.1027-1.1860.77830.204-0.05180.5375-0.8661-0.4030.4447-0.0835-0.04490.38170.06640.50693.218516.819630.4649
141.1739-1.1498-0.84980.98870.63990.5425-0.4244-0.30750.18640.1020.1144-0.014-0.0779-1.24260.50960.37720.029-0.04660.56470.06480.35161.582327.651331.5968
155.84160.19781.85993.85890.32556.92360.17880.16090.74490.6028-0.04920.1806-0.756-0.406-0.10650.45110.0310.16170.33730.07160.5249-8.086470.546237.7599
164.4680.1375-2.45281.2994-0.73633.06950.17580.12340.29410.4070.110.1651-0.5425-0.1288-0.29040.454-0.01060.03910.29110.02820.35673.427570.991528.7467
174.28430.9159-0.1394.36410.48352.2282-0.027-0.1056-0.29690.0980.009-0.4123-0.0405-0.076-0.0010.3565-0.06170.01550.40560.06150.2948.883664.290324.6311
182.70451.4950.15422.8925-0.00266.81290.2833-0.19630.28620.3327-0.02730.5144-0.5019-0.7671-0.22810.37810.05630.06480.36750.02990.4821-10.702164.785238.9387
191.2082-0.7314-0.95265.92380.20842.76650.1693-0.35270.2890.7103-0.2139-0.6845-0.5996-0.0487-0.03890.598-0.0517-0.16970.4354-0.10190.47566.779155.97557.5068
204.20411.6879-0.07263.9655-0.0282.29030.2343-0.192-0.00180.7493-0.2617-0.11550.15260.20530.10110.2935-0.0013-0.00480.2315-0.09010.2417-0.89947.709954.1512
213.32350.1361.03324.7481-0.79835.2436-0.1410.78680.0081-0.05820.19890.5470.03640.06140.14530.2905-0.01710.02480.2292-0.11050.3597-10.388144.212151.2059
224.22550.7554-0.65585.17060.00172.6003-0.0409-0.10530.15420.29110.020.27920.14870.13560.04770.45310.04240.01570.2958-0.02350.2516-8.008844.486358.3695
232.2520.7668-1.53914.3697-0.28493.07430.0120.2009-0.05580.4581-0.0205-0.1884-0.11240.0735-0.02020.35830.0113-0.10670.2989-0.03380.28310.574549.375555.5134
243.9403-1.6905-2.55399.44271.20724.08230.37950.7305-0.3022-0.1775-0.1485-0.1634-0.14350.1598-0.15210.26250.0417-0.05280.487-0.02670.474411.147155.069847.7617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 104 )A67 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 142 )A105 - 142
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 184 )A143 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 196 )A185 - 196
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 244 )A197 - 244
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 277 )A245 - 277
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 104 )B67 - 104
8X-RAY DIFFRACTION8chain 'B' and (resid 105 through 120 )B105 - 120
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 142 )B121 - 142
10X-RAY DIFFRACTION10chain 'B' and (resid 143 through 196 )B143 - 196
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 212 )B197 - 212
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 244 )B213 - 244
13X-RAY DIFFRACTION13chain 'B' and (resid 245 through 258 )B245 - 258
14X-RAY DIFFRACTION14chain 'B' and (resid 259 through 276 )B259 - 276
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 104 )C67 - 104
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 160 )C105 - 160
17X-RAY DIFFRACTION17chain 'C' and (resid 161 through 228 )C161 - 228
18X-RAY DIFFRACTION18chain 'C' and (resid 229 through 271 )C229 - 271
19X-RAY DIFFRACTION19chain 'D' and (resid 67 through 104 )D67 - 104
20X-RAY DIFFRACTION20chain 'D' and (resid 105 through 120 )D105 - 120
21X-RAY DIFFRACTION21chain 'D' and (resid 121 through 132 )D121 - 132
22X-RAY DIFFRACTION22chain 'D' and (resid 133 through 196 )D133 - 196
23X-RAY DIFFRACTION23chain 'D' and (resid 197 through 258 )D197 - 258
24X-RAY DIFFRACTION24chain 'D' and (resid 259 through 271 )D259 - 271

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