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- PDB-6h5v: MamM CTD H264E -

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Basic information

Entry
Database: PDB / ID: 6h5v
TitleMamM CTD H264E
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: 1.49 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 H264E
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 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)12,1114
Polymers11,9011
Non-polymers2103
Water88349
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)24,2228
Polymers23,8032
Non-polymers4196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1580 Å2
ΔGint-65 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.179, 94.367, 53.090
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: 11901.365 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.49→47.18 Å / Num. obs: 15616 / % possible obs: 99.6 % / Redundancy: 8.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.9
Reflection shellResolution: 1.49→1.52 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.49→47.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.718 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22878 779 5 %RANDOM
Rwork0.19969 ---
obs0.20116 14820 99.59 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.711 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.49→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 10 49 690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019661
X-RAY DIFFRACTIONr_bond_other_d0.0020.02624
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.945896
X-RAY DIFFRACTIONr_angle_other_deg0.92331440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.213586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25123.82434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50815116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.938158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
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_it5.172.072333
X-RAY DIFFRACTIONr_mcbond_other4.7962.054332
X-RAY DIFFRACTIONr_mcangle_it6.1443.04416
X-RAY DIFFRACTIONr_mcangle_other6.3233.054417
X-RAY DIFFRACTIONr_scbond_it12.062.78328
X-RAY DIFFRACTIONr_scbond_other11.7642.786328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.0973.872478
X-RAY DIFFRACTIONr_long_range_B_refined14.23126.953708
X-RAY DIFFRACTIONr_long_range_B_other14.23227.024709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 66 -
Rwork0.38 1025 -
obs--96.21 %
Refinement TLS params.Method: refined / Origin x: 37.952 Å / Origin y: 14.32 Å / Origin z: -0.424 Å
111213212223313233
T0.0823 Å20.0019 Å2-0.0143 Å2-0.0353 Å2-0.0153 Å2--0.033 Å2
L1.6484 °2-0.4138 °2-0.3792 °2-4.5784 °22.1337 °2--3.1315 °2
S0.0054 Å °-0.239 Å °0.1235 Å °0.1724 Å °0.0819 Å °-0.0909 Å °0.0003 Å °0.0505 Å °-0.0873 Å °

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