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- PDB-6h9p: MamM CTD E289D - Manganese form -

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Basic information

Entry
Database: PDB / ID: 6h9p
TitleMamM CTD E289D - Manganese form
ComponentsMagnetosome protein MamM, Cation efflux protein family
KeywordsMETAL TRANSPORT / Cation diffusion facilitator / magnetotactic bacteria
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
BETA-MERCAPTOETHANOL / : / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarber-Zucker, S. / Zarivach, R.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation 167/16 Israel
Israel Ministry of Science, Technology and Space Israel
CitationJournal: To Be Published
Title: MamM CTD E289D - Manganese form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnetosome protein MamM, Cation efflux protein family
B: Magnetosome protein MamM, Cation efflux protein family
C: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1108
Polymers35,6893
Non-polymers4215
Water1,54986
1
A: Magnetosome protein MamM, Cation efflux protein family
hetero molecules

A: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2518
Polymers23,7932
Non-polymers4586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area2900 Å2
ΔGint-43 kcal/mol
Surface area9700 Å2
MethodPISA
2
B: Magnetosome protein MamM, Cation efflux protein family
C: Magnetosome protein MamM, Cation efflux protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9854
Polymers23,7932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-32 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.261, 78.261, 175.495
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA213 - 2903 - 80
21HISHISBB213 - 2903 - 80
12GLYGLYAA211 - 2901 - 80
22GLYGLYCC211 - 2901 - 80
13HISHISBB213 - 2903 - 80
23HISHISCC213 - 2903 - 80

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Magnetosome protein MamM, Cation efflux protein family / MamM protein


Mass: 11896.372 Da / Num. of mol.: 3 / Mutation: E289D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M LiSO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 2.09→44.28 Å / Num. obs: 19491 / % possible obs: 99 % / Redundancy: 17.6 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.5
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 442 / CC1/2: 0.837 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 2.1→44.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.86 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23924 805 4.9 %RANDOM
Rwork0.21405 ---
obs0.21534 15614 84.39 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 45.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 20 86 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192017
X-RAY DIFFRACTIONr_bond_other_d0.0020.021896
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9322735
X-RAY DIFFRACTIONr_angle_other_deg1.02434363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33923.137102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.681525
X-RAY DIFFRACTIONr_chiral_restr0.1090.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02409
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7612.4041018
X-RAY DIFFRACTIONr_mcbond_other1.762.4031017
X-RAY DIFFRACTIONr_mcangle_it2.7353.5881271
X-RAY DIFFRACTIONr_mcangle_other2.7343.5891272
X-RAY DIFFRACTIONr_scbond_it2.4742.819999
X-RAY DIFFRACTIONr_scbond_other2.4352.82999
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9444.0961461
X-RAY DIFFRACTIONr_long_range_B_refined6.32929.4132142
X-RAY DIFFRACTIONr_long_range_B_other6.32529.2052130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45220.09
12B45220.09
21A46740.11
22C46740.11
31B44340.11
32C44340.11
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 30 -
Rwork0.285 523 -
obs--39.7 %
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)
13.47751.1951-1.59492.2806-2.47078.6106-0.0595-0.0139-0.0676-0.1345-0.1747-0.26620.22030.57350.23420.0419-0.00290.01330.07280.0050.044827.557-28.855-8.574
26.6302-0.1582.9155.3948-1.04056.18890.0048-0.20090.0962-0.048-0.3442-0.23150.0342-0.02730.33940.06520.00280.00380.08210.04720.048548.702-15.601-15.439
33.9368-2.40990.8897.4232-4.31494.97480.0676-0.20560.17430.2909-0.5466-0.9303-0.29270.60870.4790.0776-0.0674-0.03360.20680.14290.263260.619-1.997-21.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A211 - 302
2X-RAY DIFFRACTION2B213 - 291
3X-RAY DIFFRACTION3C211 - 291

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