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- PDB-3w60: MamM-CTD H264A -

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Basic information

Entry
Database: PDB / ID: 3w60
TitleMamM-CTD H264A
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: 1.82 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
Water93752
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
Unit cell
Length a, b, c (Å)37.358, 95.124, 53.809
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: 11919.447 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: H264A
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): Rosstea / 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.: 52 / 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: 2.01 Å3/Da / Density % sol: 38.66 % / Mosaicity: 0.882 °
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS PH 5.5, 15% PEG 3350, 0.2M 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
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 8874 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Χ2: 1.219 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.82-1.855.90.4874340.745199.8
1.85-1.895.90.5494430.932199.3
1.89-1.924.80.4184262.741197.5
1.92-1.964.70.2964173.236195
1.96-26.20.254440.9941100
2-2.055.90.1744370.846199.5
2.05-2.140.2194162.211193.1
2.1-2.165.70.1194311.057199.8
2.16-2.226.50.1064510.9091100
2.22-2.294.80.1664361.987198.9
2.29-2.376.40.0744490.8841100
2.37-2.476.50.0634450.8141100
2.47-2.586.50.0524430.8941100
2.58-2.725.90.0494561.21100
2.72-2.896.30.0394520.7451100
2.89-3.116.50.0384511.2381100
3.11-3.435.80.0464501.233197
3.43-3.9250.0624441.566198
3.92-4.945.90.0344600.997197.5
4.94-505.70.0234891.009196.3

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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: 1.82→47.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.3274 / WRfactor Rwork: 0.2552 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6639 / SU B: 11.236 / SU ML: 0.154 / SU R Cruickshank DPI: 0.1654 / SU Rfree: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.32 417 4.8 %RANDOM
Rwork0.2515 ---
obs0.2547 8756 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.72 Å2 / Biso mean: 33.5569 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2---1.33 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 10 52 683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021648
X-RAY DIFFRACTIONr_bond_other_d0.0010.02437
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.954878
X-RAY DIFFRACTIONr_angle_other_deg0.9831053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.604583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.823.43832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.99115108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.044158
X-RAY DIFFRACTIONr_chiral_restr0.1160.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02131
X-RAY DIFFRACTIONr_mcbond_it1.391.5405
X-RAY DIFFRACTIONr_mcbond_other0.4021.5165
X-RAY DIFFRACTIONr_mcangle_it2.2222652
X-RAY DIFFRACTIONr_scbond_it3.6153243
X-RAY DIFFRACTIONr_scangle_it5.2274.5225
LS refinement shellResolution: 1.815→1.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 24 -
Rwork0.398 599 -
all-623 -
obs--93.68 %
Refinement TLS params.Method: refined / Origin x: 0.4799 Å / Origin y: 14.3861 Å / Origin z: -0.2916 Å
111213212223313233
T0.0969 Å20.0474 Å2-0.0571 Å2-0.0631 Å2-0.0153 Å2--0.0661 Å2
L1.2821 °2-0.4618 °2-0.3961 °2-5.1812 °23.9285 °2--2.9942 °2
S-0.1323 Å °-0.1408 Å °0.1657 Å °0.2327 Å °0.1069 Å °0.0868 Å °0.2128 Å °0.1125 Å °0.0254 Å °

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