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- PDB-3w66: MamM-CTD D249A and H285A -

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Basic information

Entry
Database: PDB / ID: 3w66
TitleMamM-CTD D249A and H285A
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 / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / Alpha-Beta Plaits ...: / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / 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: 2.05 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 11, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnetosome protein MamM


Theoretical massNumber of molelcules
Total (without water)11,8751
Polymers11,8751
Non-polymers00
Water52229
1
A: Magnetosome protein MamM

A: Magnetosome protein MamM


Theoretical massNumber of molelcules
Total (without water)23,7512
Polymers23,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area750 Å2
ΔGint-6 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.685, 93.866, 50.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 11875.437 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: D249A, H285A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.75 Å3/Da / Density % sol: 29.56 % / Mosaicity: 0.976 °
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: SEALED TUBE / Type: Cu FINE FOCUS / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 5384 / % possible obs: 97.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.059 / Χ2: 1.025 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.095.90.3242200.895184.3
2.09-2.126.20.3122390.973189.2
2.12-2.166.40.322480.928190.2
2.16-2.216.70.3012531.026195.1
2.21-2.267.20.272520.966197.7
2.26-2.317.30.2982760.97199.6
2.31-2.377.80.2462710.993199.6
2.37-2.4380.2212640.9981100
2.43-2.580.1852791.0731100
2.5-2.588.40.1522680.9921100
2.58-2.678.20.1522761.0261100
2.67-2.788.30.122661.0211100
2.78-2.918.30.1012821.0321100
2.91-3.068.40.0782641.0321100
3.06-3.258.30.0652771.1131100
3.25-3.58.20.0522801.1071100
3.5-3.858.30.042851.0591100
3.85-4.418.20.0312790.9971100
4.41-5.558.10.0312901.0191100
5.55-257.40.0283151.1331100

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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
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w5x

3w5x


Resolution: 2.05→23.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.1667 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8436 / SU B: 9.628 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2078 / SU Rfree: 0.1875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 243 4.5 %RANDOM
Rwork0.1817 ---
obs0.1846 5347 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.29 Å2 / Biso mean: 39.6878 Å2 / Biso min: 22.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2---1.76 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 0 29 665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019674
X-RAY DIFFRACTIONr_bond_other_d0.0010.02672
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.933915
X-RAY DIFFRACTIONr_angle_other_deg0.82831528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.239590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23322.94134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8715115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.384159
X-RAY DIFFRACTIONr_chiral_restr0.10.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02164
X-RAY DIFFRACTIONr_mcbond_it3.0183.224339
X-RAY DIFFRACTIONr_mcbond_other3.0213.209338
X-RAY DIFFRACTIONr_mcangle_it4.5974.798424
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 7 -
Rwork0.205 322 -
all-329 -
obs--85.45 %
Refinement TLS params.Method: refined / Origin x: 2.1427 Å / Origin y: 14.0983 Å / Origin z: -0.1736 Å
111213212223313233
T0.0663 Å2-0.0032 Å2-0.0053 Å2-0.0148 Å2-0.0124 Å2--0.0218 Å2
L0.5461 °2-0.159 °2-0.1862 °2-1.5646 °20.3608 °2--0.186 °2
S-0.0099 Å °-0.0356 Å °0.1003 Å °0.0787 Å °0.0604 Å °-0.0549 Å °0.0619 Å °0.0348 Å °-0.0504 Å °

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