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- PDB-3w65: MamM-CTD D249A and H264A -

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Basic information

Entry
Database: PDB / ID: 3w65
TitleMamM-CTD D249A and H264A
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 ...: / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 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.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)11,9913
Polymers11,7991
Non-polymers1922
Water55831
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9836
Polymers23,5992
Non-polymers3844
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 area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.913, 94.476, 53.582
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

21A-402-

SO4

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Components

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


Mass: 11799.318 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: D249A, H264A
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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.98 Å3/Da / Density % sol: 37.87 % / Mosaicity: 0.525 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS PH=5.5, 25% PEG 3350, 0.2M AmSO4 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.37→25 Å / Num. obs: 4059 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.125 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.37-2.416.40.4082041.044199
2.41-2.456.40.3311901.1261100
2.45-2.57.30.3031941.13199.5
2.5-2.557.50.2561991.0971100
2.55-2.618.10.2751940.9951100
2.61-2.678.10.2172121.1541100
2.67-2.748.40.2061911.0711100
2.74-2.818.60.1831971.2461100
2.81-2.898.60.1621911.1961100
2.89-2.998.40.1352141.1881100
2.99-3.098.80.1141941.1151100
3.09-3.228.50.0942021.191100
3.22-3.368.60.0792081.1021100
3.36-3.548.60.0661871.1151100
3.54-3.768.60.0612111.0551100
3.76-4.058.50.0482061.1061100
4.05-4.458.60.0422021.1721100
4.45-5.098.30.0412131.121100
5.09-6.48.30.0512151.061100
6.4-257.50.0542351.1771100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w5x

3w5x


Resolution: 2.37→23.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2383 / WRfactor Rwork: 0.1788 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8015 / SU B: 15.239 / SU ML: 0.19 / SU R Cruickshank DPI: 0.3577 / SU Rfree: 0.2476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 181 4.5 %RANDOM
Rwork0.1911 ---
obs0.1936 4048 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.38 Å2 / Biso mean: 42.7441 Å2 / Biso min: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å20 Å2
2---1.5 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.37→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 10 31 673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019660
X-RAY DIFFRACTIONr_bond_other_d0.0010.02649
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.946896
X-RAY DIFFRACTIONr_angle_other_deg0.77531479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.039586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48522.81332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03715114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.222159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02152
X-RAY DIFFRACTIONr_mcbond_it2.4182.762335
X-RAY DIFFRACTIONr_mcbond_other2.392.752334
X-RAY DIFFRACTIONr_mcangle_it3.9724.11418
LS refinement shellResolution: 2.368→2.429 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 7 -
Rwork0.196 281 -
all-288 -
obs--98.29 %
Refinement TLS params.Method: refined / Origin x: 0.9049 Å / Origin y: 14.2828 Å / Origin z: -0.4143 Å
111213212223313233
T0.0824 Å20.0039 Å2-0.0337 Å2-0.0815 Å2-0.0135 Å2--0.0845 Å2
L1.4437 °2-0.7461 °2-0.4772 °2-4.1481 °21.6849 °2--3.8577 °2
S-0.0596 Å °-0.0896 Å °0.0925 Å °0.3116 Å °0.1707 Å °-0.1161 Å °0.1997 Å °0.2215 Å °-0.1111 Å °

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