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- PDB-7o3m: Crystal Structure of AcrB Single Mutant - 1 -

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Basic information

Entry
Database: PDB / ID: 7o3m
TitleCrystal Structure of AcrB Single Mutant - 1
ComponentsEfflux pump membrane transporter
KeywordsMEMBRANE PROTEIN / Multidrug Efflux Transporter
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.551 Å
AuthorsAbabou, A.
CitationJournal: To Be Published
Title: Crystal Structure of AcrB Single Mutant - 1
Authors: Ababou, A.
History
DepositionApr 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
D: Efflux pump membrane transporter
E: Efflux pump membrane transporter
F: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)697,56612
Polymers694,5026
Non-polymers3,0646
Water00
1
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,7836
Polymers347,2513
Non-polymers1,5323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-78 kcal/mol
Surface area121110 Å2
MethodPISA
2
D: Efflux pump membrane transporter
E: Efflux pump membrane transporter
F: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,7836
Polymers347,2513
Non-polymers1,5323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21350 Å2
ΔGint-79 kcal/mol
Surface area121440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.368, 156.796, 218.651
Angle α, β, γ (deg.)90.000, 92.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA2 - 104522 - 1065
2SERSERchain BBB2 - 104322 - 1063
3THRTHRchain CCC2 - 104522 - 1065
4THRTHRchain DDD2 - 104522 - 1065
5SERSERchain EEE2 - 104322 - 1063
6THRTHRchain FFF2 - 104522 - 1065

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Components

#1: Protein
Efflux pump membrane transporter


Mass: 115750.359 Da / Num. of mol.: 6 / Mutation: R620A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: acrB_4, acrB, acrB_1, acrB_2, acrB_3, acrB_5, A8C65_09270, A9819_02265, A9X72_18695, AC789_1c04620, ACN002_0478, ACN68_10695, ACN81_24630, ACU57_11680, ACU90_20590, AM270_01980, AM464_19305, ...Gene: acrB_4, acrB, acrB_1, acrB_2, acrB_3, acrB_5, A8C65_09270, A9819_02265, A9X72_18695, AC789_1c04620, ACN002_0478, ACN68_10695, ACN81_24630, ACU57_11680, ACU90_20590, AM270_01980, AM464_19305, AMK83_09190, AML35_17310, AUQ13_18190, AW059_13640, AWB10_19050, AWG78_005565, B6V57_02435, BANRA_00889, BANRA_00999, BB545_15910, BEN53_04520, BHF03_18080, BHS81_02950, BHS87_02495, BIQ87_02540, BIZ41_13825, BJJ90_19940, BK248_01725, BK292_14280, BK334_05580, BK373_00965, BK383_14595, BMA87_04530, BMT49_03610, BMT91_04935, BN17_02651, BOH76_16460, BON63_11900, BON65_19130, BON66_08715, BON69_11225, BON72_14720, BON75_11085, BON76_24190, BON86_26060, BON94_15210, BON95_06075, BON98_18530, BTQ06_00925, BUE81_06435, BvCms12BK_04863, BvCms2454_01835, BvCms28BK_00632, BvCmsC61A_03075, BvCmsHHP019_03148, BvCmsHHP056_01479, BvCmsKKP061_00163, BvCmsKSNP073_04604, BvCmsKSNP081_04683, BvCmsKSNP120_04201, BvCmsKSP011_05014, BvCmsKSP024_04861, BvCmsKSP026_02627, BvCmsKSP045_04703, BvCmsKSP058_04933, BvCmsKSP067_05122, BvCmsKSP076_04688, BvCmsNSP006_01210, BvCmsNSP007_00776, BvCmsNSP047_01693, BvCmsNSP072_02397, BvCmsOUP014_01037, BvCmsSINP011_02642, BvCmsSINP022_01605, BvCmsSIP019_03696, BvCmsSIP024_01072, BvCmsSIP044_00930, BW690_06940, BWI89_12175, BXT93_07785, BZL31_19295, C2U48_07740, C4K41_07725, C4M78_18085, C5F73_09745, C5N07_13110, C5P01_15940, C5P44_16955, C6669_02375, C6B13_10325, C7B02_04170, C7B06_13000, C7B07_14810, C9114_13235, C9160_00185, C9201_04165, C9E25_04215, C9Z03_06210, C9Z23_00255, C9Z28_08635, C9Z37_05005, C9Z43_06095, C9Z70_09245, CA593_00820, CDC27_01240, CDL37_08810, CG692_04680, CI693_16095, CI694_14685, CJU63_02500, CJU64_02490, CO706_24730, COD46_04485, CR538_19130, CR539_06565, CRD98_02045, CRM83_13415, CT146_16100, CV83915_01104, CWS33_13665, D0X26_07790, D2184_11155, D2185_12425, D3C88_31425, D3O91_18365, D4023_06520, D4628_13155, D4636_06025, D4718_02720, D4V08_10150, D6T60_09670, D6T98_07735, D6W00_12590, D6X36_16210, D7W70_07875, D7Z75_05690, D9C99_07900, D9D20_11125, D9D44_10685, D9E13_00485, D9E35_07135, D9E73_21575, D9F32_03530, D9F87_10685, D9G11_17580, D9G42_13565, D9G69_10585, D9G95_10390, D9H68_03680, D9H70_06065, D9H94_07380, D9I18_05035, D9I87_03680, D9I97_02625, D9J11_02570, D9J44_06200, D9J52_11760, D9K02_03900, D9K54_20470, D9Z28_24640, DAH18_15350, DAH30_15550, DAH34_12755, DAH37_04875, DB359_14850, DBQ99_19255, DEN89_14865, DEO04_04920, DEO20_17510, DJ503_01450, DK132_02395, DL292_07005, DL326_11785, DL479_02540, DL545_18765, DL705_13145, DLU50_07900, DLU67_10935, DLU82_01970, DLW88_19215, DLX40_09005, DLY41_06715, DLY44_14465, DM129_08550, DM267_01255, DM296_06955, DM382_09705, DM820_06155, DM973_09850, DMY83_13165, DN627_04140, DN660_06030, DN700_07110, DN808_01530, DNC98_06145, DND79_04450, DNI21_09935, DNR35_00855, DNW42_12745, DNX19_03500, DOY61_02460, DOY67_09480, DP258_04725, DP265_04400, DP277_07910, DQE91_07055, DQF36_01200, DQF57_08040, DQF72_04240, DQO13_05880, DQP61_17770, DRW19_06780, DS732_07285, DT034_10130, DTL43_07030, DTL90_18880, DTM10_06440, DU333_14630, DW236_16180, DWB25_18810, DXT69_07740, DXT71_02600, DXT73_02225, E0I42_07045, E2112_11465, E2114_15395, E2115_11930, E2119_01370, E2126_013665, E2127_09005, E2128_08320, E2129_12030, E2134_12580, E2135_12650, E2148_08850, E4K51_12425, E4K53_09525, E4K55_09900, E4K60_11595, E5P24_11315, E5P28_18315, E5S38_06395, E5S42_13425, E5S56_04760, EA184_13145, EA218_08750, EA231_12325, EA239_15375, EA250_11755, EA429_15685, EAI46_01035, EAI52_03305, EAN77_07570, EAX79_06460, EB476_04025, EB525_RS00175, EBP16_12895, EC1094V2_3386, EC382_09135, ECONIH1_02500, ECTO6_03638, ED307_06795, ED648_02095, EEP23_01410, EG075_08750, EG796_01740, EH186_13990, EHD79_03845, EI021_20720, EI028_12150, EI032_07905, EI041_08500, EIA08_09625, EIA21_12180, EJC75_24510, EL75_3290, EL79_3385, EL80_3339, ELT58_12170, ELV08_01140, ELY05_12005, EO241_14205, EPT01_06710, EQ825_17705, ERS085365_02371, ERS085366_03391, ERS085374_02303, ERS085379_01141, ERS139211_01948, ERS150873_01787, ExPECSC038_03243, EXX06_12030, EXX13_09300, EXX23_10330, EXX24_02235, EXX53_07265, EXX55_11505, EXX71_19130, EXX87_11195, EYD11_17095, EYV18_09780, EYX82_01500, EYY27_15910, EYY78_02330, F0L67_19110, F1E19_02810, F7D02_16410, F7D05_04960, F7D06_01285, F7F11_07205, F7F56_10820, F9040_08845, F9X20_11065, F9Z74_08955, FNW97_02200, FORC82_3586, FQ022_06350, FQ915_11580, FQU83_20500, FQZ46_14155, FRV13_04215, FV293_05765, FV438_08525, FZN30_08470, G5603_08575, G5608_10915, G5616_17800, G5632_14455, G5686_06550, G5688_07040, G6Z99_23720, GII66_02845, GII67_09125, GJD95_17980, GJD96_18145, GKF34_11195, GKF39_01530, GKF52_13635, GKF74_01825, GKF86_04555, GKF89_04410, GKG12_03295, GNZ03_09590, GNZ05_01310, GP650_17935, GP654_09140, GP666_11010, GP678_16470, GP689_14290, GP698_14015, GP700_10545, GP720_06095, GP727_13610, GP912_14175, GP935_15175, GP945_16670, GP946_00315, GQA06_04590, GQA63_01155, GQE22_08970, GQE30_17545, GQE33_07470, GQE34_01120, GQE42_04545, GQE51_10380, GQE58_13150, GQE64_19110, GQE87_01345, GQE93_05675, GQF59_01155, GQM10_04910, GQM17_15105, GQM18_02835, GQM28_04965, GQN16_06365, GQN24_05120, GQY14_07730, GRW05_06170, GRW12_18865, GRW30_01790, GRW42_02940, GRW80_13135, GRW81_04465, GUB85_11530, GUB91_14860, GUB95_14530, GUC01_07830, GUC12_14650, HmCms184_01943, HmCmsJML079_00721, HmCmsJML146_03063, HmCmsJML204_02413, HV022_17585, HV065_00570, HV109_17760, HV156_07455, HV159_09410, HV168_09095, HV260_09570, HVW04_08645, HVW93_05405, HVX75_18315, HVY01_17180, HVY77_19520, HVY93_17640, HVZ12_18550, HVZ21_17725, HVZ53_18305, HW43_05935, HX136_19170, HXS78_16775, MJ49_04125, MS6198_04670, MS8345_00466, NCTC10418_05566, NCTC10865_04672, NCTC10963_03279, NCTC11126_00116, NCTC11181_01060, NCTC13148_06601, NCTC13216_02965, NCTC13846_03608, NCTC9007_00190, NCTC9036_03767, NCTC9045_04279, NCTC9055_00632, NCTC9058_03192, NCTC9062_04550, NCTC9111_03904, NCTC9117_04708, NCTC9119_03922, NCTC9434_02883, NCTC9706_01042, NCTC9969_03956, PGD_02849, PU06_12600, RG28_02520, RK56_026290, RX35_02133, SAMEA3472043_02753, SAMEA3472044_00392, SAMEA3472047_02966, SAMEA3472055_02089, SAMEA3472056_03557, SAMEA3472070_02210, SAMEA3472080_01739, SAMEA3472090_01741, SAMEA3472108_01933, SAMEA3472114_01186, SAMEA3484427_03472, SAMEA3484429_01960, SAMEA3485101_03912, SAMEA3752553_00212, SAMEA3752557_00298, SAMEA3752559_02826, SAMEA3752620_00857, SAMEA3753064_01307, SAMEA3753097_00439, SAMEA3753164_00290, SAMEA3753290_01796, SAMEA3753300_00529, SK85_00486, TUM18780_32140, UN86_09270, UN91_18355, WP2S18E08_34660, WP5S18E08_35960, WP7S17E04_32630, WQ89_01050, WR15_04005
Production host: Escherichia coli (E. coli) / References: UniProt: E2QH56
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
Has ligand of interestN

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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: 3.83 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES PH 6.5, 0.2 M MGAC, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.55→98.85 Å / Num. obs: 123979 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 102.14 Å2 / Rpim(I) all: 0.066 / Net I/σ(I): 9.2
Reflection shellResolution: 3.55→3.74 Å / Num. unique obs: 18034 / Rpim(I) all: 0.392

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIF

2gif


Resolution: 3.551→19.953 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3591 6134 4.99 %
Rwork0.2765 116832 -
obs0.2807 122966 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.4 Å2 / Biso mean: 42.6355 Å2 / Biso min: 1.5 Å2
Refinement stepCycle: final / Resolution: 3.551→19.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47582 0 210 0 47792
Biso mean--30.07 --
Num. residues----6260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01448708
X-RAY DIFFRACTIONf_angle_d1.86366130
X-RAY DIFFRACTIONf_chiral_restr0.087806
X-RAY DIFFRACTIONf_plane_restr0.0098430
X-RAY DIFFRACTIONf_dihedral_angle_d17.00417606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A28956X-RAY DIFFRACTION19.65TORSIONAL
12B28956X-RAY DIFFRACTION19.65TORSIONAL
13C28956X-RAY DIFFRACTION19.65TORSIONAL
14D28956X-RAY DIFFRACTION19.65TORSIONAL
15E28956X-RAY DIFFRACTION19.65TORSIONAL
16F28956X-RAY DIFFRACTION19.65TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.551-3.59060.45091890.3522368895
3.5906-3.63260.43122170.33553937100
3.6326-3.67670.38141870.32483829100
3.6767-3.72290.41332170.32633900100
3.7229-3.77160.41282070.3343888100
3.7716-3.82290.44712150.34293904100
3.8229-3.87710.42061950.32523837100
3.8771-3.93450.41222060.32923888100
3.9345-3.99550.40052030.31843923100
3.9955-4.06050.40332090.31163893100
4.0605-4.12990.36151950.29663950100
4.1299-4.20430.38152090.30123874100
4.2043-4.28440.37362170.29453847100
4.2844-4.3710.37962060.28943921100
4.371-4.4650.35231880.28973903100
4.465-4.56770.37282190.29223864100
4.5677-4.68050.37871910.28643911100
4.6805-4.80530.38392060.28183882100
4.8053-4.94460.36391990.27113931100
4.9446-5.10160.34662150.26843885100
5.1016-5.28070.36572070.2853891100
5.2807-5.48790.3722060.29073913100
5.4879-5.7320.41042050.29033879100
5.732-6.02640.37641990.26463945100
6.0264-6.39220.35882070.26083915100
6.3922-6.86710.35772030.2633931100
6.8671-7.52430.32242060.24493926100
7.5243-8.53750.28562080.21113946100
8.5375-10.48950.26582000.20723958100
10.4895-19.9530.31532030.2497387397

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