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- PDB-3w61: MamM-CTD H285A -

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Basic information

Entry
Database: PDB / ID: 3w61
TitleMamM-CTD 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)12,1123
Polymers11,9191
Non-polymers1922
Water1,40578
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2236
Polymers23,8392
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area740 Å2
ΔGint-6 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.084, 95.078, 53.802
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: 11919.447 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: 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: 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.: 78 / 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: 1.99 Å3/Da / Density % sol: 38.17 % / Mosaicity: 0.28 °
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS PH 5.5, 25% PEG 3350, 0.2M LiSO4 , VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 13193 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.04 / Χ2: 0.854 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.59-1.625.70.2746370.715199.2
1.62-1.656.10.2516580.681100
1.65-1.6860.2176460.7021100
1.68-1.7160.1846470.7211100
1.71-1.756.10.1476530.7051100
1.75-1.7960.1216350.7541100
1.79-1.846.10.1086720.7311100
1.84-1.8960.0836440.7631100
1.89-1.9460.0626510.741100
1.94-260.0576510.7551100
2-2.0760.0476590.7451100
2.07-2.1660.0396570.7551100
2.16-2.266.10.0376630.741100
2.26-2.3860.0326590.721100
2.38-2.5260.0316690.7651100
2.52-2.7260.0366660.7781100
2.72-2.9960.0556681.1281100
2.99-3.435.90.066731.267199.9
3.43-4.325.80.0326831.889199.9
4.32-505.20.0237021.042194.6

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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: 1.59→47.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2218 / WRfactor Rwork: 0.1889 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.863 / SU B: 3.204 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0808 / SU Rfree: 0.0835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 645 4.9 %RANDOM
Rwork0.1794 ---
obs0.181 13117 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.82 Å2 / Biso mean: 24.8398 Å2 / Biso min: 13.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.59→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 10 78 709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021668
X-RAY DIFFRACTIONr_bond_other_d0.0020.02460
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.965906
X-RAY DIFFRACTIONr_angle_other_deg0.96531113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.068587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70222.64734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7915116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7031510
X-RAY DIFFRACTIONr_chiral_restr0.1170.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_mcbond_it1.4791.5408
X-RAY DIFFRACTIONr_mcbond_other0.4641.5166
X-RAY DIFFRACTIONr_mcangle_it2.4962660
X-RAY DIFFRACTIONr_scbond_it4.1113260
X-RAY DIFFRACTIONr_scangle_it6.4454.5242
LS refinement shellResolution: 1.588→1.629 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 61 -
Rwork0.26 878 -
all-939 -
obs--98.63 %
Refinement TLS params.Method: refined / Origin x: 0.4258 Å / Origin y: 14.1092 Å / Origin z: -0.4171 Å
111213212223313233
T0.0364 Å20.0025 Å2-0.0144 Å2-0.04 Å2-0.0219 Å2--0.0547 Å2
L0.0618 °2-0.3015 °2-0.0881 °2-2.0331 °21.3957 °2--1.741 °2
S0.0084 Å °-0.0157 Å °0.0361 Å °0.0846 Å °0.0691 Å °0.0034 Å °0.1547 Å °0.073 Å °-0.0775 Å °

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