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- PDB-6h88: MamM CTD D249N -

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Basic information

Entry
Database: PDB / ID: 6h88
TitleMamM CTD D249N
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 / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
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 D249N
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9882
Polymers11,9091
Non-polymers781
Water1,33374
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)23,9754
Polymers23,8192
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2110 Å2
ΔGint-14 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.488, 62.826, 44.297
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-561-

HOH

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Components

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


Mass: 11909.413 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.: 74 / 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: 1.65 Å3/Da / Density % sol: 25.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH=7.5, 25% PEG 3350, 1.7mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.5→42.01 Å / Num. obs: 12949 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Net I/σ(I): 22.2
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.814 / % possible all: 91

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.5→42.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.802 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22658 648 5 %RANDOM
Rwork0.1821 ---
obs0.18426 12290 99.04 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 22.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20 Å2
2--0.12 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.5→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms644 0 4 74 722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019668
X-RAY DIFFRACTIONr_bond_other_d0.0020.02632
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.926904
X-RAY DIFFRACTIONr_angle_other_deg0.80431456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.468587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20723.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03615115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.126158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02763
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_it1.3851.217339
X-RAY DIFFRACTIONr_mcbond_other1.2621.209338
X-RAY DIFFRACTIONr_mcangle_it2.0551.817423
X-RAY DIFFRACTIONr_mcangle_other2.061.819424
X-RAY DIFFRACTIONr_scbond_it2.8711.563329
X-RAY DIFFRACTIONr_scbond_other2.8441.563329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0862.214480
X-RAY DIFFRACTIONr_long_range_B_refined5.97716.673731
X-RAY DIFFRACTIONr_long_range_B_other5.97516.709732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.496→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 39 -
Rwork0.376 852 -
obs--93.49 %
Refinement TLS params.Method: refined / Origin x: -9.664 Å / Origin y: -4.617 Å / Origin z: -11.355 Å
111213212223313233
T0.0186 Å2-0.0226 Å2-0.0014 Å2-0.043 Å20.0011 Å2--0.0246 Å2
L1.4417 °20.431 °2-0.0509 °2-3.9212 °2-0.4667 °2--1.1402 °2
S0.1022 Å °-0.1761 Å °-0.0657 Å °0.1007 Å °-0.114 Å °0.1166 Å °0.0639 Å °-0.134 Å °0.0118 Å °

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