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- PDB-6h5u: MamM CTD H264E - Zinc form 2 -

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Basic information

Entry
Database: PDB / ID: 6h5u
TitleMamM CTD H264E - Zinc form 2
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 / : / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 H264E - Zinc form 2
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _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

Downloads & links

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


Theoretical massNumber of molelcules
Total (without water)48,22812
Polymers47,6054
Non-polymers6238
Water2,864159
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)24,2828
Polymers23,8032
Non-polymers4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2420 Å2
ΔGint-92 kcal/mol
Surface area10020 Å2
MethodPISA
2
B: Magnetosome protein MamM, Cation efflux protein family
H: Magnetosome protein MamM, Cation efflux protein family
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)36,0878
Polymers35,7043
Non-polymers3835
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area3460 Å2
ΔGint-85 kcal/mol
Surface area9570 Å2
MethodPISA
3
C: Magnetosome protein MamM, Cation efflux protein family
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)24,1867
Polymers23,8032
Non-polymers3835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area2170 Å2
ΔGint-77 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.049, 55.648, 63.767
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

21C-515-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA212 - 3002 - 90
21SERSERBB212 - 3002 - 90
12ARGARGAA212 - 2912 - 81
22ARGARGCC212 - 2912 - 81
13ARGARGBB212 - 2912 - 81
23ARGARGCC212 - 2912 - 81

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 11901.365 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Chain H is a short peptide from the protein that cannot be assigned to any of the other chains in certain.
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: mamM, mgI491, MGR_4095 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.64 Å3/Da / Density % sol: 24.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH=6.5, 25% PEG 3350, 1.7 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2→47.03 Å / Num. obs: 20715 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Rrim(I) all: 0.087 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 13.9 / CC1/2: 0.993 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 2→47.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.858 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22053 906 4.4 %RANDOM
Rwork0.17031 ---
obs0.17238 19808 98.72 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 30.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å2-0.04 Å2
2---1.04 Å20 Å2
3---1.8 Å2
Refinement stepCycle: 1 / Resolution: 2→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 25 159 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171944
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6562934
X-RAY DIFFRACTIONr_angle_other_deg1.0161.6434565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88121.353133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3211524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
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_it2.1921.4111096
X-RAY DIFFRACTIONr_mcbond_other2.1921.4111095
X-RAY DIFFRACTIONr_mcangle_it2.9852.0951368
X-RAY DIFFRACTIONr_mcangle_other2.9842.0951369
X-RAY DIFFRACTIONr_scbond_it3.9791.9651076
X-RAY DIFFRACTIONr_scbond_other3.9761.9651076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.442.7371564
X-RAY DIFFRACTIONr_long_range_B_refined7.48818.382312
X-RAY DIFFRACTIONr_long_range_B_other7.48918.3972313
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)
11A25910.11
12B25910.11
21A22550.12
22C22550.12
31B21870.12
32C21870.12
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 75 -
Rwork0.165 1424 -
obs--97.27 %
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)
12.4405-0.75030.31075.1567-1.23082.52550.0519-0.24-0.17490.1803-0.0026-0.15650.15450.0715-0.04930.0402-0.0116-0.01170.05710.0070.04075.343-13.5028.675
25.82171.5397-0.6342.20420.45532.7738-0.04680.2409-0.0606-0.1829-0.009-0.1034-0.02730.0630.05590.0521-0.0108-0.00030.03060.01460.017816.6911.10313.043
34.2769-1.8494-0.35294.1265-0.55292.58850.06230.27450.3559-0.1358-0.0192-0.0496-0.3332-0.1244-0.04310.06710.00660.00920.08890.0410.045829.965-3.82434.997
411.7721-4.8271-0.16811.26215.19516.74710.4723-0.1780.3516-0.2027-0.1305-0.4977-0.31120.2024-0.34180.2341-0.10870.10540.3707-0.05830.165224.20720.21321.14
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A212 - 301
2X-RAY DIFFRACTION2B212 - 302
3X-RAY DIFFRACTION3C211 - 292
4X-RAY DIFFRACTION4H302 - 307

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