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- PDB-3w63: MamM-CTD 215-293 -

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Basic information

Entry
Database: PDB / ID: 3w63
TitleMamM-CTD 215-293
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 / 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)9,3613
Polymers9,1681
Non-polymers1922
Water1,62190
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7216
Polymers18,3372
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area680 Å2
ΔGint-6 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.940, 95.616, 54.031
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: 9168.422 Da / Num. of mol.: 1 / Fragment: UNP residues 215-293
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.: 90 / 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: 2.6 Å3/Da / Density % sol: 52.73 % / Mosaicity: 0.409 °
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 LiSO4 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: 1.9→25 Å / Num. obs: 7854 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.301 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.936.40.4143770.9991100
1.93-1.976.60.4953860.9911100
1.97-2.016.50.4193831.4021100
2.01-2.056.50.3093900.9271100
2.05-2.096.40.3073751.0651100
2.09-2.146.60.2273911.0621100
2.14-2.196.50.2243921.2311100
2.19-2.256.50.2193861.5361100
2.25-2.326.50.2043941.5191100
2.32-2.396.50.1513731.1311100
2.39-2.486.50.1363921.1991100
2.48-2.586.50.1113931.1461100
2.58-2.76.40.0953981.26199.7
2.7-2.846.40.0783961.2921100
2.84-3.016.40.0733851.2441100
3.01-3.256.40.0683911.5691100
3.25-3.576.40.0763961.4871100
3.57-4.096.10.0884071.867199.3
4.09-5.146.10.074101.5821100
5.14-255.70.0684391.519198.2

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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: 1.9→24.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2249 / WRfactor Rwork: 0.1747 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8393 / SU B: 7.397 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1407 / SU Rfree: 0.1407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 363 4.7 %RANDOM
Rwork0.1788 ---
obs0.1813 7788 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.66 Å2 / Biso mean: 25.1428 Å2 / Biso min: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2---1.4 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms613 0 10 90 713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021658
X-RAY DIFFRACTIONr_bond_other_d0.0050.02445
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.943896
X-RAY DIFFRACTIONr_angle_other_deg1.02631079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.526586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11223.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97515117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.253159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02133
X-RAY DIFFRACTIONr_mcbond_it1.111.5403
X-RAY DIFFRACTIONr_mcbond_other0.3551.5164
X-RAY DIFFRACTIONr_mcangle_it1.9422653
X-RAY DIFFRACTIONr_scbond_it3.2843255
X-RAY DIFFRACTIONr_scangle_it5.4514.5239
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 20 -
Rwork0.214 503 -
all-523 -
obs--92.24 %
Refinement TLS params.Method: refined / Origin x: -0.2428 Å / Origin y: -14.4217 Å / Origin z: -0.3884 Å
111213212223313233
T0.0278 Å2-0.0094 Å20.0187 Å2-0.0581 Å20.0273 Å2--0.0761 Å2
L0.32 °2-0.2511 °20.2344 °2-3.0049 °2-1.5252 °2--2.5736 °2
S0.0354 Å °-0.0532 Å °-0.0982 Å °-0.0251 Å °0.0365 Å °-0.0016 Å °-0.0058 Å °-0.0967 Å °-0.0719 Å °

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