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- PDB-6h8i: MamM CTD H285D -

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Basic information

Entry
Database: PDB / ID: 6h8i
TitleMamM CTD H285D
ComponentsMagnetosome protein MamM, Cation efflux protein family
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria
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 ...: / 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
BETA-MERCAPTOETHANOL / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBarber-Zucker, S. / Zarivach, R.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation 167/16 Israel
Israel Ministry of Science, Technology and Space Israel
CitationJournal: To Be Published
Title: MamM CTD H285D
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1584
Polymers11,8871
Non-polymers2703
Water1,06359
1
A: Magnetosome protein MamM, Cation efflux protein family
hetero molecules

A: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3158
Polymers23,7752
Non-polymers5416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1760 Å2
ΔGint-82 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.445, 94.117, 53.073
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, Cation efflux protein family / MamM protein


Mass: 11887.339 Da / Num. of mol.: 1
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) / Variant (production host): Rosetta / 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: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.91 Å3/Da / Density % sol: 35.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M (NH4)2SO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 1.4→47.06 Å / Num. obs: 18410 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 858 / CC1/2: 0.639 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.4→47.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.373 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18536 898 4.9 %RANDOM
Rwork0.15844 ---
obs0.15975 17494 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 26.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0 Å2
2--0.54 Å20 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.4→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 14 59 693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019690
X-RAY DIFFRACTIONr_bond_other_d0.0020.02654
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.951942
X-RAY DIFFRACTIONr_angle_other_deg0.96431509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29723.24337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0415123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7951510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02142
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_it2.0032.275339
X-RAY DIFFRACTIONr_mcbond_other1.9752.266338
X-RAY DIFFRACTIONr_mcangle_it2.2393.398428
X-RAY DIFFRACTIONr_mcangle_other2.2393.407429
X-RAY DIFFRACTIONr_scbond_it2.5663.001351
X-RAY DIFFRACTIONr_scbond_other2.5283.002351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0894.29510
X-RAY DIFFRACTIONr_long_range_B_refined3.76129.143755
X-RAY DIFFRACTIONr_long_range_B_other3.75829.189756
X-RAY DIFFRACTIONr_rigid_bond_restr2.62731344
X-RAY DIFFRACTIONr_sphericity_free28.102539
X-RAY DIFFRACTIONr_sphericity_bonded12.39951353
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 65 -
Rwork0.268 1247 -
obs--98.8 %

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