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

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Basic information

Entry
Database: PDB / ID: 4mrp
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / PHOSPHATE ION / ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _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: ABC transporter related protein
B: ABC transporter related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,67512
Polymers136,7622
Non-polymers1,91210
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17200 Å2
ΔGint-102 kcal/mol
Surface area53050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)321.853, 95.262, 79.010
Angle α, β, γ (deg.)90.00, 102.01, 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


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


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 246 / 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: 4.33 Å3/Da / Density % sol: 71.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion / 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, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 79820 / % possible obs: 98.7 %

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
REFMAC(rigid body)refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
REFMAC(rigid body)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.736 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 3959 4.99 %PHENIX
Rwork0.2021 ---
obs0.2035 79384 98.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 124 246 9673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099589
X-RAY DIFFRACTIONf_angle_d1.22213009
X-RAY DIFFRACTIONf_dihedral_angle_d14.763476
X-RAY DIFFRACTIONf_chiral_restr0.0761510
X-RAY DIFFRACTIONf_plane_restr0.0071652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5-2.53050.45811490.46642546254693
2.5305-2.56250.47051370.42312664266497
2.5625-2.59630.40371360.38532646264698
2.5963-2.63180.39681400.36162697269797
2.6318-2.66940.37811480.34622616261698
2.6694-2.70920.341620.322712271298
2.7092-2.75160.31771280.30232713271398
2.7516-2.79670.33791290.29822630263096
2.7967-2.84490.36121350.29942630263097
2.8449-2.89660.33311650.27292701270199
2.8966-2.95230.29771250.26322725272599
2.9523-3.01250.27861470.24982690269099
3.0125-3.0780.32481440.2582751275199
3.078-3.14960.3051440.25232686268699
3.1496-3.22830.25871350.24932700270099
3.2283-3.31560.27471360.22262676267698
3.3156-3.41310.25221410.20762699269998
3.4131-3.52320.23031450.20322626262697
3.5232-3.6490.22191600.18752732273299
3.649-3.7950.22531370.170927252725100
3.795-3.96760.19331280.16572764276499
3.9676-4.17650.2221350.16582719271999
4.1765-4.43790.20761520.15972661266197
4.4379-4.780.18111550.15382678267897
4.78-5.26010.1521310.15152761276199
5.2601-6.0190.1981310.185127622762100
6.019-7.57470.19461350.19672707270797
7.5747-39.74110.20531490.18162808280898
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)
13.15290.00411.35711.5479-0.42951.18980.1021-0.3342-0.34340.1958-0.00720.27620.1043-0.3666-0.0490.3878-0.01660.10340.55040.04180.554523.784725.180990.4836
20.22790.4067-0.10260.48080.06240.5229-0.01740.0471-0.0959-0.0194-0.00160.19610.0461-0.2915-0.04250.4008-0.0306-0.02930.56410.06920.71728.425817.956571.7995
31.8952-0.4112-0.16052.9219-0.51451.78320.05760.12580.4403-0.1583-0.0909-0.5746-0.15790.2363-0.0040.3816-0.04440.06320.3424-0.09350.59277.536324.146698.7229
43.69160.0931-1.53591.6734-0.16131.2216-0.0260.36160.0581-0.14770.08130.05620.0007-0.4569-0.07450.4084-0.0165-0.07690.6052-0.00080.430524.979630.786759.4404
50.5089-0.5080.33530.3518-0.07970.47770.0053-0.07060.1324-0.01450.00950.09030.059-0.2573-0.03190.44250.00970.06410.61150.04820.801728.515338.0578.3037
62.7270.43140.26433.41650.24361.33180.0659-0.1725-0.20920.3863-0.0007-0.17550.11440.0657-0.05130.40570.01280.01960.3139-0.04070.244179.481331.09856.9272
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 340 )
3X-RAY DIFFRACTION3chain 'A' and (resid 341 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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