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- PDB-6h8a: MamM CTD D249N - Cadmium form -

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Basic information

Entry
Database: PDB / ID: 6h8a
TitleMamM CTD D249N - Cadmium form
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 / plasma membrane
Similarity search - Function
: / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain ...: / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / 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: 1.8 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 - Cadmium form
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)12,2925
Polymers11,9091
Non-polymers3834
Water99155
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)24,58410
Polymers23,8192
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1880 Å2
ΔGint-94 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.844, 94.661, 53.438
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: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 37.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Li2SO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7mM CdCl2

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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: 1.8→47.33 Å / Num. obs: 9025 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 533 / CC1/2: 0.666 / % possible all: 100

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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: 1.8→47.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.304 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23669 908 10.1 %RANDOM
Rwork0.19241 ---
obs0.1968 8103 100 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.058 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2--0.44 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 15 55 692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019671
X-RAY DIFFRACTIONr_bond_other_d0.0030.02633
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.939910
X-RAY DIFFRACTIONr_angle_other_deg0.7663.0011457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.078587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83423.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58615118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.736159
X-RAY DIFFRACTIONr_chiral_restr0.090.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
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_it0.8951.692330
X-RAY DIFFRACTIONr_mcbond_other0.8921.686329
X-RAY DIFFRACTIONr_mcangle_it1.4512.52414
X-RAY DIFFRACTIONr_mcangle_other1.4492.527415
X-RAY DIFFRACTIONr_scbond_it2.252.061341
X-RAY DIFFRACTIONr_scbond_other2.2322.06341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6022.976494
X-RAY DIFFRACTIONr_long_range_B_refined5.69521.285726
X-RAY DIFFRACTIONr_long_range_B_other5.69821.372727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 63 -
Rwork0.337 606 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 37.442 Å / Origin y: 14.151 Å / Origin z: -0.523 Å
111213212223313233
T0.0296 Å2-0.0079 Å2-0.0175 Å2-0.0203 Å2-0.0255 Å2--0.0841 Å2
L1.1272 °2-0.7526 °2-0.3737 °2-6.9353 °22.9679 °2--4.5759 °2
S0.1042 Å °-0.1424 Å °0.1359 Å °0.0743 Å °0.0761 Å °-0.0765 Å °0.1865 Å °0.1175 Å °-0.1803 Å °

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