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- PDB-3nog: Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plastic... -

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Basic information

Entry
Database: PDB / ID: 3nog
TitleDesigned ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface
Components
  • Acriflavine resistance protein B
  • Designed ankyrin repeat protein
KeywordsTRANSPORT PROTEIN/PROTEIN BINDING / membrane protein / RND / drug-efflux pump / transport protein / designed ankyrin repeat protein / crystallization chaperone / TRANSPORT PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.34 Å
AuthorsMonroe, N. / Briand, C. / Gruetter, M.G.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface
Authors: Monroe, N. / Sennhauser, G. / Seeger, M.A. / Briand, C. / Grutter, M.G.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acriflavine resistance protein B
B: Acriflavine resistance protein B
C: Acriflavine resistance protein B
D: Designed ankyrin repeat protein
E: Designed ankyrin repeat protein


Theoretical massNumber of molelcules
Total (without water)377,4825
Polymers377,4825
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.400, 158.000, 258.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acriflavine resistance protein B


Mass: 113693.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Protein Designed ankyrin repeat protein


Mass: 18201.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1blue

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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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG4000, (NH4)2SO4, ADA, pH 6.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2007
RadiationMonochromator: Si 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 576037 / Rmerge(I) obs: 0.143 / D res high: 3.34 Å / Num. obs: 86836 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
78318299.810.047
67561299.910.081
561095610010.102
4.65736499.910.109
4.34.6740099.810.151
44.3982699.810.219
3.641861699.810.364
3.343.61726699.710.556
ReflectionResolution: 3.34→50 Å / Num. all: 87029 / Num. obs: 86836 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 6.63 % / Biso Wilson estimate: 70.68 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 14.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) allRsym value% possible all
3.34-3.66.50.3630.5563.91129301731117266172660.6040.60499.7
3.6-46.80.2360.3646.21262001864718616186160.3940.39499.8
4-4.36.90.1330.21910.3676809841982698260.2370.23799.8
4.3-4.66.60.0990.15113.8487727414740074000.1640.16499.8
4.6-56.60.0710.10917.9484687372736473640.1180.11899.9
5-66.90.0630.10219.1751191096110956109560.1110.111100
6-76.40.0540.08122359705618561256120.0890.08999.9
7-86.30.030.04732.2201963189318231820.0510.05199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8S

2j8s


Resolution: 3.34→48.776 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7187 / SU ML: 0.56 / Isotropic thermal model: TLS / σ(F): 1.99 / σ(I): -3 / Phase error: 33.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3075 1043 1.2 %RANDOM
Rwork0.257 ---
obs0.2576 86818 99.8 %-
all-87029 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.731 Å2 / ksol: 0.245 e/Å3
Displacement parametersBiso max: 477.45 Å2 / Biso mean: 80.1192 Å2 / Biso min: 23.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.0467 Å20 Å20 Å2
2---1.925 Å20 Å2
3---1.9717 Å2
Refinement stepCycle: LAST / Resolution: 3.34→48.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24874 0 0 0 24874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01825332
X-RAY DIFFRACTIONf_angle_d1.64534524
X-RAY DIFFRACTIONf_chiral_restr0.1014163
X-RAY DIFFRACTIONf_plane_restr0.0114449
X-RAY DIFFRACTIONf_dihedral_angle_d15.7818806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3401-3.51610.40791480.3381211412262
3.5161-3.73630.37541470.30361210512252
3.7363-4.02470.34041470.27191211412261
4.0247-4.42950.31521480.23791221112359
4.4295-5.06980.29121490.21281223712386
5.0698-6.38520.30651490.25811232512474
6.3852-48.78080.25021550.24241266812823
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)
10.06030.10140.18820.01980.08810.15050.093-0.24640.05690.0524-0.0702-0.02340.0196-0.19920.02110.180.01880.06530.6609-0.06470.303326.2917-37.2793-16.6244
20.434-0.31830.15840.5654-0.00080.23960.1289-0.36840.10740.03520.0840.0459-0.0144-0.0694-0.07660.06560.04610.15840.2514-0.15220.285424.26362.972-24.3233
30.2080.0331-0.24810.1217-0.01730.23620.2079-0.2168-0.03420.015-0.0608-0.0305-0.01990.17830.00430.2416-0.10230.00430.9048-0.0530.255439.8618-35.46235.7899
40.0993-0.2657-0.06450.95820.09470.032-0.0421-0.02340.0892-0.1836-0.1239-0.092-0.1388-0.1998-0.00830.26180.29950.0064-0.0486-0.42310.452733.94318.165-30.0199
50.32130.24150.08890.1977-0.0570.12730.01250.3529-0.1602-0.01490.0095-0.19730.0655-0.0124-0.01520.17570.06-0.02960.6065-0.15660.391542.4361-53.1534-41.4184
60.4449-0.1675-0.15650.469-0.00890.7943-0.01510.54040.136-0.1434-0.07850.00030.1471-0.40690.1190.13210.113-0.10070.4927-0.05710.309228.0439-15.8304-78.1914
70.33870.2733-0.03670.41230.13260.1772-0.0610.5142-0.0571-0.05540.10830.06240.0717-0.1842-0.02290.248-0.0012-0.12210.5986-0.20530.331520.8307-59.3831-42.0096
80.43110.4919-0.0860.73460.08690.3489-0.19190.19780.1131-0.08830.60840.1221-0.111-0.0533-0.20440.1086-0.0202-0.12650.73490.11880.258217.4066-15.8017-74.4198
90.3182-0.0350.13650.2241-0.0650.09590.1996-0.0001-0.04330.0552-0.17060.04470.06060.1027-0.01480.1793-0.00730.03880.7489-0.01370.378554.3206-30.7368-35.5882
100.25430.03910.37450.22740.04880.7623-0.1561-0.5484-0.18890.08170.0297-0.22450.0746-0.41070.04250.1522-0.03760.0060.63190.1570.334756.9862-46.2544-0.049
110.5555-0.18460.25490.1076-0.13720.19590.02170.0008-0.01040.01180.0023-0.08960.02320.0669-0.00770.0879-0.00350.02850.3678-0.0520.294671.6652-22.7649-41.3446
121.16810.5667-0.78990.6834-0.15730.6581-0.0581-0.243-0.1518-0.0798-0.0378-0.0405-0.01970.19450.04080.3615-0.01470.11690.29760.0340.372369.6607-1.1333-82.2372
131.5810.603-0.39910.89460.48350.85160.27750.00350.46420.10620.1388-0.3124-0.0257-0.0434-0.29420.2907-0.15170.03370.31820.01370.5236-0.3762-71.4448-37.9297
141.1885-0.0647-0.14851.1035-0.2941.19130.2312-0.1502-0.0137-0.03830.1181-0.0624-0.1283-0.1166-0.20820.469-0.20260.04480.38470.15160.23511.5163-75.8387-22.828
150.0023-0.03040.0620.3787-0.72471.4138-0.3079-0.1327-0.0931-0.10460.2515-0.1056-0.2559-0.5573-0.05290.40260.0276-0.09010.8049-0.11610.30373.0681-74.8548-9.0535
160.14830.17130.02060.19750.02360.0029-0.0129-0.0237-0.014-0.01020.02630.01190.02180.0314-0.01741.24770.2018-0.39740.9783-0.31651.323436.6872-20.665626.293
170.1532-0.0216-0.18780.16410.02280.27480.0408-0.01240.06590.1517-0.4689-0.0765-0.0484-0.39890.31330.6873-0.1373-0.24981.4687-0.03750.188345.329-36.663530.929
180.04230.04210.07870.04240.07560.14870.0473-0.0133-0.06760.1023-0.0044-0.0596-0.0673-0.01590.00720.84630.0267-0.30670.75770.11060.991456.4841-53.606928.8631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:342)A1 - 342
2X-RAY DIFFRACTION2(chain A and resid 343:667)A343 - 667
3X-RAY DIFFRACTION3(chain A and resid 668:872)A668 - 872
4X-RAY DIFFRACTION4(chain A and resid 873:1049)A873 - 1049
5X-RAY DIFFRACTION5(chain B and resid 1:344)B1 - 344
6X-RAY DIFFRACTION6(chain B and resid 345:559)B345 - 559
7X-RAY DIFFRACTION7(chain B and resid 560:872)B560 - 872
8X-RAY DIFFRACTION8(chain B and resid 873:1049)B873 - 1049
9X-RAY DIFFRACTION9(chain C and resid 1:132)C1 - 132
10X-RAY DIFFRACTION10(chain C and resid 133:263)C133 - 263
11X-RAY DIFFRACTION11(chain C and resid 264:1018)C264 - 1018
12X-RAY DIFFRACTION12(chain C and resid 1019:1049)C1019 - 1049
13X-RAY DIFFRACTION13(chain D and resid 1:76)D1 - 76
14X-RAY DIFFRACTION14(chain D and resid 77:114)D77 - 114
15X-RAY DIFFRACTION15(chain D and resid 115:169)D115 - 169
16X-RAY DIFFRACTION16(chain E and resid 1:34)E1 - 34
17X-RAY DIFFRACTION17(chain E and resid 35:136)E35 - 136
18X-RAY DIFFRACTION18(chain E and resid 137:169)E137 - 169

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