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- PDB-4mrn: Structure of a bacterial Atm1-family ABC transporter -

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Basic information

Entry
Database: PDB / ID: 4mrn
TitleStructure of a bacterial Atm1-family ABC transporter
ComponentsABC transporter related protein
KeywordsTRANSPORT PROTEIN / Membrane Protein / Substrate exporter / heavy metal resistance / Membrane
Function / homology
Function and homology information


Translocases / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLee, J.Y. / Yang, J.G. / Zhitnitsky, D. / Lewinson, O. / Rees, D.C.
CitationJournal: Science / Year: 2014
Title: Structural basis for heavy metal detoxification by an Atm1-type ABC exporter.
Authors: Lee, J.Y. / Yang, J.G. / Zhitnitsky, D. / Lewinson, O. / Rees, D.C.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter related protein
B: ABC transporter related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,25012
Polymers136,7622
Non-polymers1,48710
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-96 kcal/mol
Surface area53460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)320.775, 95.498, 79.670
Angle α, β, γ (deg.)90.00, 101.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ABC transporter related protein


Mass: 68381.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: ATM1, Saro_2631 / Plasmid: pET15b, pJL-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q2G506
#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 4.37 Å3/Da / Density % sol: 71.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 100 mM sodium citrate pH 5.4, 200 mM magnesium acetate, and 12% w/v polyethylene glycol 5,000 mono methyl ether, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97906, 0.97927, 1.00000
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979271
311
ReflectionResolution: 2.5→40 Å / Num. obs: 80410 / % possible obs: 98.7 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→39.796 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 4013 5.02 %Phenix
Rwork0.1996 ---
obs0.201 79876 97.91 %-
all-82596 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 94 289 9686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099559
X-RAY DIFFRACTIONf_angle_d1.23312973
X-RAY DIFFRACTIONf_dihedral_angle_d14.9013464
X-RAY DIFFRACTIONf_chiral_restr0.0771506
X-RAY DIFFRACTIONf_plane_restr0.0081644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5-2.52940.41561580.422368236891
2.5294-2.56030.44121300.40852560256096
2.5603-2.59270.43431340.3872580258096
2.5927-2.62680.38981440.40272536253697
2.6268-2.66270.37721390.35182604260498
2.6627-2.70080.3391480.34962578257898
2.7008-2.74110.32451480.32422615261598
2.7411-2.78390.38061250.3122572257297
2.7839-2.82950.38011360.31032594259496
2.8295-2.87830.35171440.30052610261099
2.8783-2.93060.33641340.272639263999
2.9306-2.9870.29991290.25552674267499
2.987-3.04790.25931510.25242633263399
3.0479-3.11420.29731380.23632613261399
3.1142-3.18660.28611400.23582665266599
3.1866-3.26620.2591310.22662602260298
3.2662-3.35450.27871400.21252608260898
3.3545-3.45320.2321360.20142612261297
3.4532-3.56460.25321380.19212622262298
3.5646-3.69190.21061540.18192614261499
3.6919-3.83960.21781280.17932661266199
3.8396-4.01420.21991260.17612675267599
4.0142-4.22560.22221440.16592649264999
4.2256-4.490.18121380.15112599259997
4.49-4.83610.16271490.14792606260698
4.8361-5.32180.15821320.150627122712100
5.3218-6.08950.21021200.182687268799
6.0895-7.66310.17551350.20022647264797
7.6631-39.80140.21061440.18612728272898
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)
11.579-0.04481.07450.8563-0.48570.8941-0.0429-0.103-0.42220.1660.09470.19720.046-0.6045-0.01690.3929-0.01820.04580.79090.04460.538723.824125.199891.1445
20.1367-0.0486-0.08070.16910.02730.3371-0.02760.0624-0.0028-0.01390.05840.20480.0263-0.3956-0.03350.3853-0.0914-0.00260.55820.00950.54635.641917.086578.7705
31.6385-0.2882-0.08882.7297-0.8481.54930.08870.08910.307-0.2215-0.0921-0.5974-0.19680.2125-0.03230.3893-0.0520.08560.2749-0.1020.566578.60926.090198.3339
42.0032-0.1862-0.89671.1947-0.17340.94210.03350.17370.0413-0.15820.0430.0460.154-0.6055-0.06280.4335-0.0795-0.10120.7767-0.01380.407324.953130.989660.064
50.2559-0.68740.31520.4691-0.19020.4436-0.0489-0.0840.0583-0.023-0.00040.05750.0915-0.46550.03340.4052-0.02140.06960.7587-0.01240.693728.458238.279679.0735
61.95410.41310.01952.74030.20231.17790.1099-0.1317-0.21710.3161-0.0207-0.22760.1080.1193-0.04820.36730.0226-0.03190.2133-0.02290.147379.13831.233857.2456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 376 )
3X-RAY DIFFRACTION3chain 'A' and (resid 377 through 607 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 183 through 340 )
6X-RAY DIFFRACTION6chain 'B' and (resid 341 through 606 )

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