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- PDB-4r86: Crystal Structure of Aminoglycoside/Multidrug Efflux System AcrD ... -

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Basic information

Entry
Database: PDB / ID: 4r86
TitleCrystal Structure of Aminoglycoside/Multidrug Efflux System AcrD from Salmonella typhimurium
ComponentsRND family aminoglycoside/multidrug efflux pump
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold
Function / homology
Function and homology information


efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / DI(HYDROXYETHYL)ETHER / Efflux pump membrane transporter
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsKim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Aminoglycoside/Multidrug Efflux System AcrD from Salmonella typhimurium
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Structure summary
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RND family aminoglycoside/multidrug efflux pump
B: RND family aminoglycoside/multidrug efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6577
Polymers66,2232
Non-polymers4345
Water1086
1
A: RND family aminoglycoside/multidrug efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2973
Polymers33,1111
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RND family aminoglycoside/multidrug efflux pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3604
Polymers33,1111
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.167, 91.167, 147.402
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein RND family aminoglycoside/multidrug efflux pump


Mass: 33111.418 Da / Num. of mol.: 2 / Fragment: AcrD domain of UNP residues 35-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: acrD, STM2481 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q8ZN77
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 47.1 % w/v PEG 1000, 150 mM Tris pH 8.0, 30 mM Potassium Bromide, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 14557 / Num. obs: 14557 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.057 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.07 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 875 / Rsym value: 0.775 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.001→45.584 Å / Isotropic thermal model: mixed / Cross valid method: throughoout / σ(F): 0 / Phase error: 22.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.224 731 5.06 %ramdom
Rwork0.186 ---
all0.188 14446 --
obs0.188 14446 98.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.5 Å2
Refinement stepCycle: LAST / Resolution: 3.001→45.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 20 6 4417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034462
X-RAY DIFFRACTIONf_angle_d0.7846051
X-RAY DIFFRACTIONf_dihedral_angle_d14.9771640
X-RAY DIFFRACTIONf_chiral_restr0.028707
X-RAY DIFFRACTIONf_plane_restr0.004805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.005-3.23650.2431430.21452611275491
3.2365-3.56120.25731400.19072724286495
3.5612-4.07420.23781350.17592728286395
4.0742-5.12450.17331560.1582751290794
5.1245-23.62140.24221520.20192843299592
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)
13.5191.18561.28573.97770.53783.52450.2286-0.85340.1390.4709-0.0751-0.41760.25780.5432-0.12610.30140.06840.01390.55280.01350.3153-26.512-30.2034-45.5821
21.5121.5011-0.02771.75660.81332.4160.2208-0.3496-0.11440.4811-0.0269-0.29620.31770.7363-0.12110.30720.0839-0.05390.61060.00810.4426-20.6943-30.1615-47.5783
31.9707-1.2912-0.18622.45611.09291.26980.04690.19520.2731-0.1134-0.0175-0.2948-0.27150.4637-0.02060.2352-0.06690.04720.38720.05940.3685-26.3871-17.0207-65.4255
42.52660.30630.04350.88570.43791.995-0.0778-0.80060.33120.29510.4126-0.5811-0.20910.6228-0.31170.29480.0939-0.00350.7662-0.13360.5947-7.6975-25.0318-57.4001
54.2063-0.90391.69010.3939-0.34810.30190.1917-0.01370.0399-0.1345-0.019-0.71480.07210.25180.01910.37620.03580.04850.7573-0.08940.39071.5084-25.2989-62.4484
62.474-0.3224-0.3067-0.01930.92850.89880.1725-0.00210.0507-0.2053-0.1737-0.4054-0.16830.1806-0.01520.4676-0.0283-0.01010.26970.08790.4308-32.065-14.9237-61.2688
72.6443-0.01-1.04474.0411-2.35027.5085-0.6747-0.19710.4110.6492-0.431-0.7796-0.772-0.86120.47920.4151-0.06810.0480.2519-0.00270.3643-36.9484-16.0493-57.6059
81.84422.2296-1.86452.7688-1.52064.69920.0259-0.6191-0.4637-0.4923-0.0434-0.1792-0.02321.04660.02880.3499-0.07030.00430.24810.03110.457-39.7225-10.0876-22.8625
96.1878-2.0342-3.00121.25191.89752.8023-0.04460.83050.4406-0.67480.7044-0.7246-0.38520.4617-0.07230.7484-0.1457-0.00080.696-0.07430.3395-38.4253-5.9535-33.8642
102.7011.2052-1.50640.94350.90371.92440.1674-0.080.5519-0.47750.134-0.0256-0.71450.4231-0.17750.7463-0.15730.03670.4214-0.00050.3258-36.5957-2.9561-26.1812
110.37490.5730.26422.3868-0.18171.0333-0.069-0.04880.09240.25080.1675-0.181-0.35970.2375-0.17590.3196-0.05460.0030.3844-0.01910.3844-27.0242-6.8496-11.4795
123.0552.7241-0.49252.74590.68344.0529-0.56660.2932-0.1055-1.84140.9166-0.61640.050.0452-0.0430.595-0.14890.05430.3593-0.07210.4629-28.5781.0133-15.6465
130.95881.63960.14252.361.23660.53760.07990.20750.0726-0.00510.1502-0.1017-0.28130.2115-0.21840.3949-0.05230.00370.44890.03190.3146-25.8863-7.3624-11.6698
142.99190.57121.7853.64940.38413.7663-0.23560.2373-0.17270.36620.30330.6913-0.40330.63870.15590.34960.07440.06030.294-0.04190.3829-31.1496-23.9332-16.112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 282 )
7X-RAY DIFFRACTION7chain 'A' and (resid 283 through 300 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 43 )
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 100 )
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 176 )
12X-RAY DIFFRACTION12chain 'B' and (resid 177 through 200 )
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 281 )
14X-RAY DIFFRACTION14chain 'B' and (resid 282 through 301 )

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