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- PDB-6h9t: MamM CTD H285D - Cadmium form -

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Basic information

Entry
Database: PDB / ID: 6h9t
TitleMamM CTD H285D - Cadmium 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 / : / 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
BETA-MERCAPTOETHANOL / : / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 H285D - Cadmium form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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.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.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_symmetry / _struct_conn_type.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2705
Polymers11,8871
Non-polymers3834
Water97354
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)24,54010
Polymers23,7752
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1940 Å2
ΔGint-90 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.366, 94.562, 53.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-403-

SO4

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Components

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


Mass: 11887.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.93 Å3/Da / Density % sol: 36.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M LiSO4, 0.1M BIS-TRIS pH=5.5, 25% PEG 3350, 1.7mM CdCl2

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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: 1.7→47.28 Å / Num. obs: 10419 / % possible obs: 99.5 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.664 / % possible all: 98.5

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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: 1.7→35.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.827 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22545 519 5 %RANDOM
Rwork0.19042 ---
obs0.19199 9895 99.14 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 32.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å20 Å2
2---0.11 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.7→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 15 54 695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.014682
X-RAY DIFFRACTIONr_bond_other_d0.0020.017606
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.67927
X-RAY DIFFRACTIONr_angle_other_deg1.0191.6391429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.927590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85420.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.67515122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.881510
X-RAY DIFFRACTIONr_chiral_restr0.0810.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02794
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02110
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_it2.1021.911336
X-RAY DIFFRACTIONr_mcbond_other2.0591.899335
X-RAY DIFFRACTIONr_mcangle_it2.982.833422
X-RAY DIFFRACTIONr_mcangle_other3.0042.844423
X-RAY DIFFRACTIONr_scbond_it4.4922.522346
X-RAY DIFFRACTIONr_scbond_other4.3892.52346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2733.588502
X-RAY DIFFRACTIONr_long_range_B_refined8.49724.138740
X-RAY DIFFRACTIONr_long_range_B_other8.54624.252741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 31 -
Rwork0.393 726 -
obs--98.95 %
Refinement TLS params.Method: refined / Origin x: 36.988 Å / Origin y: 14.146 Å / Origin z: -0.397 Å
111213212223313233
T0.0484 Å2-0.0027 Å2-0.0147 Å2-0.0281 Å2-0.0164 Å2--0.0297 Å2
L1.3207 °2-0.6862 °2-0.3305 °2-4.8994 °22.1512 °2--3.6 °2
S0.0521 Å °-0.1802 Å °0.0722 Å °0.1226 Å °0.1167 Å °-0.01 Å °0.1852 Å °0.1472 Å °-0.1688 Å °

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