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- PDB-6ha2: MamM CTD D249H-H285D -

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Basic information

Entry
Database: PDB / ID: 6ha2
TitleMamM CTD D249H-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: 1.5 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 D249H-H285D
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 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)11,9892
Polymers11,9101
Non-polymers781
Water93752
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)23,9774
Polymers23,8212
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.737, 94.302, 52.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 11910.397 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-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.87 Å3/Da / Density % sol: 34.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaAcetate pH=4.5, 25% PEG 3350, 1.7mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→47.15 Å / Num. obs: 14775 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.6
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.582 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.5→47.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.782 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19872 748 5.1 %RANDOM
Rwork0.16078 ---
obs0.16256 14008 99.68 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 30.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 4 52 668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019656
X-RAY DIFFRACTIONr_bond_other_d0.0030.02626
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.935891
X-RAY DIFFRACTIONr_angle_other_deg0.8283.0011444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.708588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45423.61136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26915117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.83159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02133
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_it2.2692.57325
X-RAY DIFFRACTIONr_mcbond_other2.2662.557324
X-RAY DIFFRACTIONr_mcangle_it2.8353.839407
X-RAY DIFFRACTIONr_mcangle_other2.8343.852408
X-RAY DIFFRACTIONr_scbond_it2.873.386331
X-RAY DIFFRACTIONr_scbond_other2.8693.386331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5854.815480
X-RAY DIFFRACTIONr_long_range_B_refined4.18232.564691
X-RAY DIFFRACTIONr_long_range_B_other4.16632.308684
X-RAY DIFFRACTIONr_rigid_bond_restr2.3831282
X-RAY DIFFRACTIONr_sphericity_free32.148536
X-RAY DIFFRACTIONr_sphericity_bonded14.83951286
LS refinement shellResolution: 1.498→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 67 -
Rwork0.285 980 -
obs--97.03 %

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