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- PDB-3w64: MamM-CTD 215-293 -

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Basic information

Entry
Database: PDB / ID: 3w64
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 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
B: Magnetosome protein MamM
D: Magnetosome protein MamM
C: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,54012
Polymers36,6744
Non-polymers8678
Water68538
1
A: Magnetosome protein MamM
C: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9157
Polymers18,3372
Non-polymers5785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Magnetosome protein MamM
D: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6255
Polymers18,3372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.966, 75.477, 88.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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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.: 4 / 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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.96 Å3/Da / Density % sol: 58.38 % / Mosaicity: 1.345 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1M BIS-TRIS PH 6.9, 25% PEG 3350, 0.2M LiSO4 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 10553 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.126 / Χ2: 1.271 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.96.30.4945201.075199.8
2.9-2.956.20.4835181.102199.2
2.95-3.016.30.3675081.062199.4
3.01-3.076.30.395061.109198.8
3.07-3.146.30.2775141.137199.6
3.14-3.216.50.2335221.092199.1
3.21-3.296.40.1975051.092199
3.29-3.386.70.1575171.1421100
3.38-3.486.60.1485261.3411100
3.48-3.596.80.1325281.1751100
3.59-3.7170.1235171.3661100
3.71-3.8670.115271.2271100
3.86-4.047.10.115341.4341100
4.04-4.257.20.095161.3041100
4.25-4.517.20.0835321.4051100
4.51-4.857.10.0835361.3141100
4.85-5.337.10.0965361.2221100
5.33-6.097.10.1175481.268199.8
6.09-7.670.0965511.3981100
7.6-206.50.0535921.94199.7

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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: 2.85→19.89 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2362 / WRfactor Rwork: 0.1931 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8339 / SU B: 29.635 / SU ML: 0.275 / SU R Cruickshank DPI: 0.3355 / SU Rfree: 0.4012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 502 4.8 %RANDOM
Rwork0.223 ---
obs0.2252 10450 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.68 Å2 / Biso mean: 23.6775 Å2 / Biso min: 3.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å20 Å20 Å2
2--6.02 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 48 38 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212586
X-RAY DIFFRACTIONr_bond_other_d0.0010.021736
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9393500
X-RAY DIFFRACTIONr_angle_other_deg1.09734197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7185324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80823.106132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.46815440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361533
X-RAY DIFFRACTIONr_chiral_restr0.0880.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
X-RAY DIFFRACTIONr_mcbond_it0.7431.51601
X-RAY DIFFRACTIONr_mcbond_other0.1281.5657
X-RAY DIFFRACTIONr_mcangle_it1.41722577
X-RAY DIFFRACTIONr_scbond_it1.583985
X-RAY DIFFRACTIONr_scangle_it2.8144.5920
Refine LS restraints NCS

Ens-ID: 1 / Number: 924 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.710.5
2BMEDIUM POSITIONAL0.650.5
3CMEDIUM POSITIONAL0.630.5
4DMEDIUM POSITIONAL0.840.5
1AMEDIUM THERMAL1.172
2BMEDIUM THERMAL0.792
3CMEDIUM THERMAL1.222
4DMEDIUM THERMAL0.812
LS refinement shellResolution: 2.852→2.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 36 -
Rwork0.33 699 -
all-735 -
obs--97.35 %
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)
12.63921.2422.27080.59761.4715.7499-0.0502-0.0682-0.066-0.0287-0.0272-0.0774-0.153-0.14040.07740.12270.03080.0050.0618-0.02630.1194-19.6032-0.925210.1386
21.95181.1629-0.50982.0669-2.46414.0106-0.11280.39230.03950.08170.0936-0.10580.1651-0.10930.01920.1247-0.0184-0.01940.11470.02880.1156-4.086-4.6515-11.1231
34.2865-1.6110.3632.7178-2.5122.5529-0.10740.10360.32590.08980.0164-0.04450.05280.09850.0910.1092-0.0069-0.02020.08320.02030.145118.7660.889-4.938
43.2901-1.5594-2.13720.60792.33136.1823-0.0766-0.298-0.01790.10880.059-0.00790.40920.1910.01760.11570.03250.02120.05430.05430.07683.293-8.0314.003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A211 - 291
2X-RAY DIFFRACTION2B213 - 293
3X-RAY DIFFRACTION3D211 - 292
4X-RAY DIFFRACTION4C214 - 291

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