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- PDB-3w5x: MamM-CTD -

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Basic information

Entry
Database: PDB / ID: 3w5x
TitleMamM-CTD
ComponentsMagnetosome protein MamM
KeywordsMETAL TRANSPORT / cation diffusion facilitator / CDF / divalent cation transport / metal ion transport
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsZeytuni, N. / Davidov, G. / Zarivach, R.
CitationJournal: Plos One / Year: 2014
Title: Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain
Authors: Zeytuni, N. / Uebe, R. / Maes, M. / Davidov, G. / Baram, M. / Raschdorf, O. / Nadav-Tsubery, M. / Kolusheva, S. / Bitton, R. / Goobes, G. / Friedler, A. / Miller, Y. / Schuler, D. / Zarivach, R.
History
DepositionFeb 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1994
Polymers11,9101
Non-polymers2883
Water1,47782
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3978
Polymers23,8212
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area730 Å2
ΔGint-6 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.882, 94.559, 53.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / / Magnetosome protein MamM / Cation efflux protein family / MamM protein


Mass: 11910.398 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Strain: MSR-1 / Gene: mamM, mgI491, MGR_4095 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 37.24 % / Mosaicity: 0.499 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 4000, 0.2M Ammonium sulfate, 0.1M Sodium acetate , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Date: Nov 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 12559 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.058 / Χ2: 2.342 / Net I/σ(I): 18.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.634.90.485141.565183.4
1.63-1.666.10.4386191.5641100
1.66-1.696.40.3666431.7021100
1.69-1.726.40.326201.7911100
1.72-1.766.40.2366361.6721100
1.76-1.86.50.2046271.6571100
1.8-1.856.40.176361.6841100
1.85-1.96.40.1316151.8891100
1.9-1.956.30.1196362.652199.8
1.95-2.026.40.0916321.9131100
2.02-2.096.30.0816392.3551100
2.09-2.176.40.0656362.1391100
2.17-2.276.20.0646272.6141100
2.27-2.396.40.0536452.1911100
2.39-2.546.40.0526392.476199.5
2.54-2.746.20.0546413.101199.8
2.74-3.015.90.0556453.783199.4
3.01-3.455.50.056513.914199.7
3.45-4.345.40.0466493.715197.2
4.34-505.10.0396092.873185.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BYP

3byp


Resolution: 1.6→47.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2043 / WRfactor Rwork: 0.1747 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8773 / SU B: 2.936 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0806 / SU Rfree: 0.0849 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 613 4.9 %RANDOM
Rwork0.1695 ---
obs0.1714 12499 98.48 %-
all-12559 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.47 Å2 / Biso mean: 25.5978 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 15 82 716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021680
X-RAY DIFFRACTIONr_bond_other_d0.0010.02455
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.941930
X-RAY DIFFRACTIONr_angle_other_deg1.08831106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.741591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87123.05636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71515119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.102159
X-RAY DIFFRACTIONr_chiral_restr0.1440.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_mcbond_it1.5511.5414
X-RAY DIFFRACTIONr_mcbond_other0.531.5168
X-RAY DIFFRACTIONr_mcangle_it2.6512673
X-RAY DIFFRACTIONr_scbond_it4.3553266
X-RAY DIFFRACTIONr_scangle_it7.174.5251
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 45 -
Rwork0.283 862 -
all-907 -
obs--98.05 %
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)
10.0564-0.69370.66450.38280.91472.1449-0.00880.06460.0690.22170.1164-0.14240.09980.1617-0.10760.04940.0062-0.01450.0764-0.03370.04394.354720.91687.5507
20.62870.1714-1.17131.90680.37363.060.0247-0.02410.11850.37210.1569-0.08650.29440.3781-0.18160.09110.0567-0.05060.0586-0.02540.0354.95977.97580.0932
36.0037-6.5435-3.43837.29261.49791.55610.56470.10770.3977-0.5379-0.245-0.3851-0.149-0.0399-0.31970.0333-0.00020.03720.0615-0.050.13052.822724.6117-3.354
45.0098-2.6383-0.61542.08530.65610.639-0.0224-0.19460.1755-0.05080.0922-0.0740.0377-0.0158-0.06990.0175-0.0055-0.00050.0642-0.03180.0856-4.531829.28384.3504
5-0.123-0.83090.28231.85840.62890.97240.1114-0.02550.031-0.08690.03780.05840.08250.053-0.14920.0470.0197-0.02850.0521-0.0370.07632.048710.4699-6.2238
6-2.1034-0.8875-1.00893.40023.63627.81420.04420.04180.2710.0446-0.16420.06090.4709-0.3080.120.1194-0.0298-0.0580.011-0.01320.0558-4.18841.9847-9.5189
7-0.49170.2382-0.27434.3113.11572.41820.0528-0.06730.07260.071-0.09410.17540.2338-0.17250.04130.0779-0.0317-0.02320.0564-0.02170.069-5.50829.53870
8-0.8251-0.63650.48853.751-1.70432.97050.04340.06310.02370.2594-0.04580.25410.139-0.11490.00240.0439-0.00670.00290.0825-0.03360.0552-5.660219.97037.0718
9-0.9632-0.95760.8165.51792.49950.64190.1090.20390.1727-0.0073-0.0967-0.14120.1175-0.0046-0.01230.04830.0382-0.00990.0762-0.01650.0682.572311.8249-7.6526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A212 - 224
2X-RAY DIFFRACTION2A225 - 236
3X-RAY DIFFRACTION3A237 - 240
4X-RAY DIFFRACTION4A241 - 246
5X-RAY DIFFRACTION5A247 - 258
6X-RAY DIFFRACTION6A259 - 264
7X-RAY DIFFRACTION7A265 - 276
8X-RAY DIFFRACTION8A277 - 283
9X-RAY DIFFRACTION9A284 - 291

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