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- PDB-3w8p: MamM-CTD D249A&H28A mutant -

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Basic information

Entry
Database: PDB / ID: 3w8p
TitleMamM-CTD D249A&H28A mutant
ComponentsMagnetosome protein MamM
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / CDF / 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: 1.8 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
DepositionMar 20, 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_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1356
Polymers23,7512
Non-polymers3844
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-59 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.560, 87.526, 64.693
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
11B-562-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 212 - 300 / Label seq-ID: 2 - 90

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / 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: pET28a / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.25 Å3/Da / Density % sol: 45.37 % / Mosaicity: 0.818 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M BIS-TRIS PH=6.2, 26% PEG 3350, 0.2M AmSO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 19801 / % possible obs: 99.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.087 / Χ2: 2.501 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8310.90.5019741.5471100
1.83-1.8610.90.4659851.6821100
1.86-1.910.70.4179742.4691100
1.9-1.9410.50.3649912.9941100
1.94-1.9810.80.2459871.7971100
1.98-2.03110.1979731.711100
2.03-2.0810.60.2049852.5161100
2.08-2.1310.90.1499932.0431100
2.13-2.210.90.1319881.9231100
2.2-2.2710.10.1489793.0231100
2.27-2.3510.80.1159962.2431100
2.35-2.4410.90.0939752.041100
2.44-2.5510.80.099892.3721100
2.55-2.6910.70.08310032.5181100
2.69-2.8610.70.089982.7621100
2.86-3.0810.50.08210093.3151100
3.08-3.399.80.08210063.801199.8
3.39-3.8790.0759853.849197.7
3.87-4.878.60.0639903.073195.8
4.87-258.80.06210213.015194.4

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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: 1.8→24.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.649 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 992 5 %RANDOM
Rwork0.2067 ---
obs0.2086 19682 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.41 Å2 / Biso mean: 35.3942 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å20 Å2
2---1.49 Å2-0 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 20 166 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191487
X-RAY DIFFRACTIONr_bond_other_d0.0060.021447
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9532027
X-RAY DIFFRACTIONr_angle_other_deg1.4233323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57823.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021697
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02335
X-RAY DIFFRACTIONr_mcbond_it2.342.353742
X-RAY DIFFRACTIONr_mcbond_other2.3362.351741
X-RAY DIFFRACTIONr_mcangle_it3.183.505929
Refine LS restraints NCS

Ens-ID: 1 / Number: 4803 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 55 -
Rwork0.22 1215 -
all-1270 -
obs--86.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7632-0.82620.62331.0894-0.17121.8393-0.0042-0.0088-0.07980.043-0.0040.110.0409-0.10250.00820.04280.0456-0.00670.07160.00640.118.01927.9982-13.5295
20.1967-0.4032-0.24531.64710.04610.58910.00630.02820.0454-0.0914-0.0328-0.1933-0.0056-0.08140.02650.08770.07060.00610.06960.0040.084926.920913.9731-35.9228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A212 - 301
2X-RAY DIFFRACTION2B212 - 301

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