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- PDB-5hsp: MamM CTD M250L -

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Basic information

Entry
Database: PDB / ID: 5hsp
TitleMamM CTD M250L
ComponentsMagnetosome protein MamM
KeywordsMETAL TRANSPORT / cation diffusion facilitator
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBarber-Zucker, S. / Zarivach, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
The Israel Ministry of Science, Technology and Space Israel
CitationJournal: Sci Rep / Year: 2016
Title: Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance.
Authors: Barber-Zucker, S. / Uebe, R. / Davidov, G. / Navon, Y. / Sherf, D. / Chill, J.H. / Kass, I. / Bitton, R. / Schuler, D. / Zarivach, R.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 16, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry / reflns_shell
Revision 1.3Jan 10, 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

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Assembly

Deposited unit
A: Magnetosome protein MamM
D: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7554
Polymers27,5632
Non-polymers1922
Water70339
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9476
Polymers27,5632
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
2
D: Magnetosome protein MamM

D: Magnetosome protein MamM


Theoretical massNumber of molelcules
Total (without water)27,5632
Polymers27,5632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)37.832, 94.914, 53.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

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Components

#1: Protein Magnetosome protein MamM / Magnetosome protein MamM / Cation efflux protein family / MamM protein


Mass: 13781.448 Da / Num. of mol.: 2 / Fragment: UNP residues 215-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M BIS-TRIS pH=5.0 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.27 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.79→47.46 Å / Num. obs: 9313 / % possible obs: 98.7 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.79→47.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.032 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 978 10.5 %RANDOM
Rwork0.19687 ---
obs0.2018 8311 98.85 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 43.794 Å2
Baniso -1Baniso -2Baniso -3
1-4.59 Å20 Å2-0 Å2
2---2.07 Å20 Å2
3----2.52 Å2
Refinement stepCycle: 1 / Resolution: 1.79→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 10 39 731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019698
X-RAY DIFFRACTIONr_bond_other_d0.0020.02676
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.945944
X-RAY DIFFRACTIONr_angle_other_deg0.91431541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.139586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32523.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79415119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.138158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
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_it2.3572.522350
X-RAY DIFFRACTIONr_mcbond_other2.3552.51349
X-RAY DIFFRACTIONr_mcangle_it3.5013.736434
X-RAY DIFFRACTIONr_mcangle_other3.4973.75435
X-RAY DIFFRACTIONr_scbond_it3.4793.105348
X-RAY DIFFRACTIONr_scbond_other3.4573.105348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3144.498511
X-RAY DIFFRACTIONr_long_range_B_refined8.04221.068740
X-RAY DIFFRACTIONr_long_range_B_other8.03821.073740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 69 -
Rwork0.379 496 -
obs--84.33 %
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)
12.0401-1.19090.79868.0439-4.02155.22170.0336-0.187-0.18580.20660.12320.172-0.015-0.1642-0.15680.1492-0.00560.01770.01940.01840.021318.465-14.614-0.307
27.9607-4.754-0.267514.17712.38224.34730.13830.4471-0.2108-0.44760.0807-0.34510.4692-0.0853-0.2190.25670.01220.00080.2552-0.06130.273420.968-28.433-8.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A212 - 291
2X-RAY DIFFRACTION2D2 - 9

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