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- PDB-6g6i: MamM CTD W247A -

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Basic information

Entry
Database: PDB / ID: 6g6i
TitleMamM CTD W247A
ComponentsMagnetosome protein MamM
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: 2.4 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: Febs J. / Year: 2019
Title: Metal binding to the dynamic cytoplasmic domain of the cation diffusion facilitator (CDF) protein MamM induces a 'locked-in' configuration.
Authors: Barber-Zucker, S. / Hall, J. / Mangapuram, S.V. / Kass, I. / Kolusheva, S. / MacMillan, F. / Zarivach, R. / Henn, A.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnetosome protein MamM
B: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6693
Polymers23,5912
Non-polymers781
Water41423
1
B: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM


Theoretical massNumber of molelcules
Total (without water)23,6693
Polymers23,5912
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.652, 65.754, 68.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 212 - 305 / Label seq-ID: 2 - 95

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11795.266 Da / Num. of mol.: 2
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-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.: 23 / 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: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS pH=5.5, 20% PEG 3350

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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: 2.4→47.49 Å / Num. obs: 7305 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.068 / Rrim(I) all: 0.205 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.498.71.57190.6650.5281.59497.2
8.96-47.496.70.0521790.9990.020.05699.8

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 2.4→47.49 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 24.548 / SU ML: 0.256 / SU R Cruickshank DPI: 1.8039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.804 / ESU R Free: 0.323
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 844 11.6 %RANDOM
Rwork0.221 ---
obs0.2258 6427 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 129.4 Å2 / Biso mean: 45.995 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--1.73 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2.4→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 4 23 1551
Biso mean--79.39 34.49 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191569
X-RAY DIFFRACTIONr_bond_other_d0.0010.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9452121
X-RAY DIFFRACTIONr_angle_other_deg0.7123.0013410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96824.02677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18415271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0271516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
Refine LS restraints NCS

Ens-ID: 1 / Number: 2573 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.395→2.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 53 -
Rwork0.314 459 -
all-512 -
obs--95.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3075-1.48131.17475.5111-2.50633.3396-0.07640.12080.2058-0.18730.0470.2077-0.2693-0.09120.02930.0971-0.0194-0.0060.0747-0.03760.10265.6371.83819.747
24.26450.9169-2.30883.0545-2.13647.9659-0.09540.28290.2472-0.24310.16790.1267-0.1109-0.2787-0.07250.06710.0204-0.0490.0543-0.01240.0732-15.79761.2818.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A211 - 306
2X-RAY DIFFRACTION2B212 - 315

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