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- PDB-3w5z: MamM-CTD D249A -

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Basic information

Entry
Database: PDB / ID: 3w5z
TitleMamM-CTD D249A
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: 1.66 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 1.3Nov 20, 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)12,1584
Polymers11,9431
Non-polymers2153
Water99155
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3158
Polymers23,8852
Non-polymers4306
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 area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.294, 94.794, 53.390
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: 11942.506 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: D249A
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.92 Å3/Da / Density % sol: 36.02 % / Mosaicity: 0.143 °
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M MES pH 5.2, 20% PEG 4000, 0.15M AmSO4 , 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: 1.66→50 Å / Num. obs: 11245 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.038 / Χ2: 1.062 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.66-1.698.40.5315450.6271100
1.69-1.7290.4645520.6211100
1.72-1.7590.3915660.6431100
1.75-1.798.90.2675430.6851100
1.79-1.8390.2545490.7231100
1.83-1.879.10.1995580.7481100
1.87-1.928.90.155530.9281100
1.92-1.9790.1235420.9951100
1.97-2.0390.1035740.951100
2.03-2.098.90.0825481.0581100
2.09-2.1790.065580.9131100
2.17-2.2590.0575660.9031100
2.25-2.3690.0495480.9541100
2.36-2.4890.0415700.8951100
2.48-2.638.90.0365670.9711100
2.63-2.848.90.0365651.2041100
2.84-3.128.80.0415692.1021100
3.12-3.588.50.045872.5971100
3.58-4.58.50.0265821.5841100
4.5-507.80.0236031.135196

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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: 1.66→47.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2388 / WRfactor Rwork: 0.1946 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8551 / SU B: 4.055 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0976 / SU Rfree: 0.1002 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 537 4.8 %RANDOM
Rwork0.1914 ---
obs0.1931 11230 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.67 Å2 / Biso mean: 29.4623 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2---0.96 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.66→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms623 0 11 55 689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021669
X-RAY DIFFRACTIONr_bond_other_d0.0020.02455
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.959908
X-RAY DIFFRACTIONr_angle_other_deg1.00831104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.601587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0422.94134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4115115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.493159
X-RAY DIFFRACTIONr_chiral_restr0.120.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
X-RAY DIFFRACTIONr_mcbond_it1.3931.5408
X-RAY DIFFRACTIONr_mcbond_other0.4631.5166
X-RAY DIFFRACTIONr_mcangle_it2.4412660
X-RAY DIFFRACTIONr_scbond_it4.1513261
X-RAY DIFFRACTIONr_scangle_it6.4174.5244
LS refinement shellResolution: 1.659→1.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 48 -
Rwork0.307 746 -
all-794 -
obs--96.48 %
Refinement TLS params.Method: refined / Origin x: 0.1725 Å / Origin y: 14.1682 Å / Origin z: -0.3867 Å
111213212223313233
T0.0543 Å20.001 Å2-0.0167 Å2-0.0546 Å2-0.0416 Å2--0.069 Å2
L-0.0008 °2-0.341 °2-0.0374 °2-2.0877 °20.8944 °2--1.6939 °2
S0.037 Å °-0.047 Å °0.0552 Å °0.0446 Å °0.0571 Å °0.0172 Å °0.1478 Å °0.0614 Å °-0.0941 Å °

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