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- PDB-4z3p: MATE transporter ClbM in complex with Rb+ -

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Basic information

Entry
Database: PDB / ID: 4z3p
TitleMATE transporter ClbM in complex with Rb+
ComponentsPutative drug/sodium antiporter
KeywordsTRANSPORT PROTEIN / transporter
Function / homologyMulti antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / membrane / CACODYLATE ION / RUBIDIUM ION / Drug/sodium antiporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMousa, J.J. / Bruner, S.D.
CitationJournal: Nat Microbiol / Year: 2016
Title: MATE transport of the E. coli-derived genotoxin colibactin.
Authors: Mousa, J.J. / Yang, Y. / Tomkovich, S. / Shima, A. / Newsome, R.C. / Tripathi, P. / Oswald, E. / Bruner, S.D. / Jobin, C.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative drug/sodium antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4873
Polymers55,2651
Non-polymers2222
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.220, 80.220, 175.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative drug/sodium antiporter


Mass: 55264.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clbM / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q0P7K3
#2: Chemical ChemComp-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.8
Details: 30% PEG 500 DME, 100 mM lithium sulfate, 400 mM rubidium chloride, 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→43.81 Å / Num. obs: 10052 / % possible obs: 97.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.8
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn


Resolution: 3.3→39.099 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 1009 10.08 %
Rwork0.1982 --
obs0.2069 10006 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→39.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 6 1 3352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123425
X-RAY DIFFRACTIONf_angle_d1.54657
X-RAY DIFFRACTIONf_dihedral_angle_d14.4831182
X-RAY DIFFRACTIONf_chiral_restr0.055566
X-RAY DIFFRACTIONf_plane_restr0.007551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.47410.36651350.23151261X-RAY DIFFRACTION97
3.4741-3.69160.30331430.21251270X-RAY DIFFRACTION98
3.6916-3.97640.26341440.19281281X-RAY DIFFRACTION98
3.9764-4.37610.26441400.17121254X-RAY DIFFRACTION95
4.3761-5.00820.25361460.16821291X-RAY DIFFRACTION98
5.0082-6.30560.32581450.22251278X-RAY DIFFRACTION95
6.3056-39.10170.28791560.21161362X-RAY DIFFRACTION96

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