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- PDB-6h84: MamM CTD D249H - Cadmium form -

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Basic information

Entry
Database: PDB / ID: 6h84
TitleMamM CTD D249H - 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 / 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: 2.04 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 - Cadmium form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 1, 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)12,3165
Polymers11,9331
Non-polymers3834
Water39622
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)24,63210
Polymers23,8672
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1980 Å2
ΔGint-93 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.493, 94.516, 53.303
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-403-

SO4

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Components

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


Mass: 11933.457 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M AmSu, 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: ID23-1 / Wavelength: 0.977999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977999 Å / Relative weight: 1
ReflectionResolution: 2.04→47.26 Å / Num. obs: 6119 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Net I/σ(I): 13.9
Reflection shellResolution: 2.04→2.1 Å / CC1/2: 0.603 / % possible all: 95.6

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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: 2.04→47.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.081 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22206 591 9.7 %RANDOM
Rwork0.18967 ---
obs0.19291 5517 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 40.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.48 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 2.04→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms634 0 15 22 671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019660
X-RAY DIFFRACTIONr_bond_other_d0.0020.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.937892
X-RAY DIFFRACTIONr_angle_other_deg1.00331425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.279583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45923.0333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09115113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.595158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02132
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_it2.082.572329
X-RAY DIFFRACTIONr_mcbond_other2.0652.563328
X-RAY DIFFRACTIONr_mcangle_it3.1573.821410
X-RAY DIFFRACTIONr_mcangle_other3.1543.831411
X-RAY DIFFRACTIONr_scbond_it2.9363.158331
X-RAY DIFFRACTIONr_scbond_other2.7573.124323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6714.476470
X-RAY DIFFRACTIONr_long_range_B_refined7.39530.431666
X-RAY DIFFRACTIONr_long_range_B_other7.44130.537667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 37 -
Rwork0.252 373 -
obs--95.13 %
Refinement TLS params.Method: refined / Origin x: 37.152 Å / Origin y: 14.406 Å / Origin z: -0.457 Å
111213212223313233
T0.0158 Å2-0.0041 Å2-0.0135 Å2-0.0264 Å2-0.0087 Å2--0.0494 Å2
L1.7165 °2-0.7376 °2-0.5289 °2-6.639 °23.0476 °2--4.8063 °2
S0.0478 Å °-0.151 Å °0.1439 Å °0.1472 Å °0.1199 Å °-0.0725 Å °0.1198 Å °0.1831 Å °-0.1677 Å °

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