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- PDB-6h87: MamM CTD D249N - Zinc form -

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Basic information

Entry
Database: PDB / ID: 6h87
TitleMamM CTD D249N - Zinc 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 / 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 / CARBON DIOXIDE / Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 D249N - Zinc form
Authors: Barber-Zucker, S. / Zarivach, R.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2286
Polymers11,9091
Non-polymers3185
Water1,45981
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)24,45612
Polymers23,8192
Non-polymers63710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2390 Å2
ΔGint-189 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.137, 53.137, 64.465
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-549-

HOH

31A-563-

HOH

41A-578-

HOH

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Components

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


Mass: 11909.413 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 (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH=8.5, 0.3M MgFormate, 1.7mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.5→46.02 Å / Num. obs: 17417 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.3
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.933 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.5→46.02 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.355 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22706 873 5 %RANDOM
Rwork0.18928 ---
obs0.19122 16518 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å2-0 Å2
2---0.34 Å20 Å2
3---1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.5→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms699 0 10 81 790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019793
X-RAY DIFFRACTIONr_bond_other_d0.0020.02743
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9241080
X-RAY DIFFRACTIONr_angle_other_deg0.95731717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44522.85742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78415139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6581511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02172
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_it3.7021.209391
X-RAY DIFFRACTIONr_mcbond_other3.6231.202390
X-RAY DIFFRACTIONr_mcangle_it4.6731.809496
X-RAY DIFFRACTIONr_mcangle_other4.6761.813497
X-RAY DIFFRACTIONr_scbond_it18.6342.159402
X-RAY DIFFRACTIONr_scbond_other17.6442.142400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.4532.746580
X-RAY DIFFRACTIONr_long_range_B_refined17.43218.585932
X-RAY DIFFRACTIONr_long_range_B_other17.43218.625933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.497→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 63 -
Rwork0.4 1173 -
obs--97.17 %
Refinement TLS params.Method: refined / Origin x: -18.578 Å / Origin y: -5.901 Å / Origin z: -1.889 Å
111213212223313233
T0.0178 Å20.0004 Å20.0115 Å2-0.022 Å20.0004 Å2--0.0761 Å2
L4.5549 °20.4206 °2-0.9959 °2-1.869 °2-0.5132 °2--2.3083 °2
S-0.0972 Å °-0.1715 Å °-0.102 Å °0.1477 Å °0.0121 Å °0.1127 Å °0.0487 Å °-0.1416 Å °0.0851 Å °

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