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- PDB-6qek: Putative membrane tansporter, magnetosome protein MamM CTD [Desul... -

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Basic information

Entry
Database: PDB / ID: 6qek
TitlePutative membrane tansporter, magnetosome protein MamM CTD [Desulfamplus magnetovallimortis BW-1]
ComponentsMagnetosome protein
KeywordsTRANSPORT PROTEIN / Bacterial organelle / cation diffusion facilitators / iron transport / magnetosome biogenesis / structure-function analysis.
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain
Similarity search - Domain/homology
Biological speciesDesulfamplus magnetovallimortis BW-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKeren, N.K. / Zarivach, R.Z.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation167/16 Israel
CitationJournal: To Be Published
Title: Putative membrane tansporter, magnetosome protein MamM CTD [Desulfamplus magnetovallimortis BW-1]
Authors: Keren, N.K. / Zarivach, R.Z.
History
DepositionJan 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Magnetosome protein
B: Magnetosome protein


Theoretical massNumber of molelcules
Total (without water)17,8452
Polymers17,8452
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint4 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.019, 47.019, 130.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Magnetosome protein


Mass: 8922.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfamplus magnetovallimortis BW-1 (bacteria)
Gene: mamM
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8IQT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 3,350 0.1M BIS-TRIS pH 5.5 0.2M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.773
11-K, -H, -L20.227
ReflectionResolution: 1.85→40.72 Å / Num. obs: 13784 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MamM CTD MSR-1

Resolution: 1.95→40.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.153 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 574 4.8 %RANDOM
Rwork0.20668 ---
obs0.20958 11291 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.845 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2--2.81 Å20 Å2
3----5.63 Å2
Refinement stepCycle: 1 / Resolution: 1.95→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 48 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191216
X-RAY DIFFRACTIONr_bond_other_d0.0040.021210
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.9511653
X-RAY DIFFRACTIONr_angle_other_deg1.12232798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08425.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28415223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.749157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2293.989620
X-RAY DIFFRACTIONr_mcbond_other4.2233.984619
X-RAY DIFFRACTIONr_mcangle_it5.3865.955772
X-RAY DIFFRACTIONr_mcangle_other5.3835.961773
X-RAY DIFFRACTIONr_scbond_it4.8664.607596
X-RAY DIFFRACTIONr_scbond_other4.8624.611597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.226.686881
X-RAY DIFFRACTIONr_long_range_B_refined8.83148.2711274
X-RAY DIFFRACTIONr_long_range_B_other8.82448.2571271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 51 -
Rwork0.235 818 -
obs--99.89 %

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