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- PDB-3noc: Designed ankyrin repeat protein (DARPin) binders to AcrB: Plastic... -

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Basic information

Entry
Database: PDB / ID: 3noc
TitleDesigned ankyrin repeat protein (DARPin) binders to AcrB: Plasticity of the Interface
Components
  • Acriflavine resistance protein B
  • Designed ankyrin repeat proteinDARPin
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 / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / outer membrane-bounded periplasmic space / membrane / identical protein binding / 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: 2.7 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

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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)377,6975
Polymers377,6975
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.854, 158.924, 245.169
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 / DARPin


Mass: 18308.611 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 3.76 Å3/Da / Density % sol: 67.3 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2007 / Details: mirrors
RadiationMonochromator: double Si 111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 156357 / Num. obs: 154751 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.47 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.7-34.510.5562.95417050.62999.5
3-44.550.1878.12650790.2199.2
4-54.430.05822.31232130.06698.6
5-64.580.05723.21103830.06599.1
6-104.360.03332.04111890.03797.5
10-504.140.0250.831990.02395.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2j8s


Resolution: 2.7→49.21 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.785 / SU ML: 0.41 / Isotropic thermal model: TLS / σ(F): 2 / σ(I): -3 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1548 1 %RANDOM
Rwork0.2423 ---
obs0.2426 154197 99 %-
all-156357 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.804 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso max: 279.36 Å2 / Biso mean: 61.9465 Å2 / Biso min: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1--8.825 Å20 Å20 Å2
2--8.4351 Å20 Å2
3---0.3899 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25120 0 0 438 25558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925590
X-RAY DIFFRACTIONf_angle_d0.80834844
X-RAY DIFFRACTIONf_dihedral_angle_d12.3388956
X-RAY DIFFRACTIONf_chiral_restr0.0584170
X-RAY DIFFRACTIONf_plane_restr0.0044482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.78720.40051400.376513857100
2.7872-2.88680.34641390.33891376499
2.8868-3.00230.33271400.319113925100
3.0023-3.13890.34461410.29913922100
3.1389-3.30440.32961410.286313945100
3.3044-3.51140.30511390.25391375798
3.5114-3.78240.24971410.22421393799
3.7824-4.16290.22781410.20481394799
4.1629-4.76480.21531400.18521384798
4.7648-6.00150.22481420.21031408499
6.0015-49.2180.24551440.22871421897
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)
10.18290.1015-0.10990.11350.06080.27770.0643-0.0392-0.00840.0346-0.01280.03730.01350.0292-0.03540.2110.0053-0.00080.3774-0.02810.238526.2797-37.7467-15.8478
20.55090.145-0.07780.37630.04670.33380.11-0.08440.1907-0.0501-0.07970.1147-0.17770.0599-0.03310.27160.07330.05230.299-0.03430.347723.93993.1022-23.8897
30.63520.4494-0.28130.690.09820.29980.1397-0.47080.08440.0555-0.13550.00580.00940.08340.02670.2423-0.0481-0.01240.6115-0.1120.237140.3617-35.29435.2349
40.9858-0.1187-0.3590.30730.28810.75250.076-0.0990.3987-0.18630.01110.0939-0.3182-0.0733-0.13940.69840.09170.08040.4477-0.11270.677134.313118.8071-29.3912
50.39160.13830.03750.0317-0.0430.13610.07630.1678-0.0837-0.016-0.0631-0.01890.01990.0996-0.00510.2110.0407-0.02990.3536-0.03920.229842.5274-54.4466-39.1052
60.614-0.340.29180.9503-0.08450.36770.00590.43720.1316-0.1125-0.00860.08640.0487-0.147-0.01540.28730.0359-0.01920.61130.15380.281528.1978-16.5478-75.024
70.2502-0.0379-0.06620.69450.17860.09850.05840.2193-0.0863-0.1538-0.03120.0977-0.0344-0.0757-0.02120.2578-0.0031-0.06660.4623-0.09210.290120.8428-60.519-39.7162
80.30960.12030.31920.3126-0.23230.90170.00230.12040.1323-0.04340.14450.24870.03730.0185-0.11840.34810.0578-0.0530.58220.12280.420917.4874-16.6983-71.0931
90.3312-0.6352-0.03511.922-0.40760.04020.15320.1764-0.15410.1701-0.19510.46250.0110.01620.03210.2534-0.04130.03740.3874-0.01360.303254.5376-30.9842-33.8985
100.42780.0643-0.13060.06610.2190.38190.0066-0.4799-0.00340.1133-0.0522-0.137-0.02040.14990.06610.1881-0.01-0.00120.55980.09970.318457.1789-46.81810.3079
110.29340.00940.12070.2607-0.23130.23010.00190.06180.0179-0.00010.00480.004-0.01290.0980.00170.2464-0.0183-0.00360.44880.05240.253671.9714-23.4628-39.3717
121.28960.65760.02290.75510.20080.0854-0.29360.2009-0.0405-0.23860.35210.0282-0.20020.1253-0.02860.4866-0.1516-0.0550.75710.10420.451671.6906-3.9221-75.7245
131.2970.2942-0.82840.6356-0.01631.35340.13220.37450.2626-0.1136-0.06690.27520.0128-0.74240.09440.2956-0.0506-0.0630.5173-0.12330.4492-0.548-72.7265-35.2575
140.2058-0.5778-0.16171.7028-0.00031.5849-0.20980.2579-0.09660.1894-0.00090.2478-0.0064-0.31510.2150.4067-0.0935-0.03040.5674-0.04540.46711.2926-77.1437-20.5971
150.4335-0.61210.55540.8661-0.74221.7883-0.194-0.63650.0854-0.05860.2984-0.25660.0767-0.641-0.08790.5181-0.0773-0.12110.8969-0.08860.4943.0645-75.8352-7.6918
160.6272-0.0982-0.04930.02570.0050.0158-0.26640.2561-0.0049-0.0701-0.0895-0.060.0299-0.29230.21140.7723-0.0006-0.18060.8637-0.35610.815538.442-22.251225.1973
170.4332-0.37220.42070.6165-0.30150.3725-0.056-0.3414-0.02240.6057-0.2113-0.3120.3535-0.55560.19960.5896-0.243-0.06571.2304-0.14290.308246.3217-37.456329.6784
180.0502-0.10590.00250.2582-0.03010.01050.383-0.24260.0022-0.3265-0.0798-0.25910.3081-0.2606-0.28440.60790.0613-0.15521.05480.16910.379357.6232-53.95226.3954
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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