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- PDB-5ho1: MamB-CTD -

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Basic information

Entry
Database: PDB / ID: 5ho1
TitleMamB-CTD
ComponentsMagnetosome protein MamB
KeywordsSIGNALING PROTEIN / C-terminal domain / Magnetotactic bacteria / metallochaperone like domain / cation diffusion facilitator / Metal-binding site
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding
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
Magnetosome protein MamB
Similarity search - Component
Biological speciesMagnetospira sp. QH-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsKeren, N. / Zarivach, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Ministry of Science, Technology and Space Israel
CitationJournal: Mol. Microbiol. / Year: 2018
Title: The dual role of MamB in magnetosome membrane assembly and magnetite biomineralization.
Authors: Uebe, R. / Keren-Khadmy, N. / Zeytuni, N. / Katzmann, E. / Navon, Y. / Davidov, G. / Bitton, R. / Plitzko, J.M. / Schuler, D. / Zarivach, R.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.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_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 MamB
B: Magnetosome protein MamB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9665
Polymers22,7692
Non-polymers1963
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-101 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.556, 49.828, 95.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 210 - 290 / Label seq-ID: 19 - 99

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Magnetosome protein MamB


Mass: 11384.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospira sp. QH-2 (bacteria) / Gene: mamB, MGMAQ_1061 / Production host: Escherichia coli (E. coli) / References: UniProt: W6KHH6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 27% PEG 3350, 0.1 M HEPES pH 7.6, 0.2 M Ammonium sulfate, 5 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.273 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.273 Å / Relative weight: 1
ReflectionResolution: 2.53→47.94 Å / Num. obs: 6527 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.7
Reflection shellResolution: 2.53→2.65 Å / Rmerge(I) obs: 1.822

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HO5

5ho5


Resolution: 2.53→47.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 40.015 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.111 / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29414 628 9.7 %RANDOM
Rwork0.23957 ---
obs0.24489 5832 98.33 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 95.457 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å2-0 Å2
2--4.57 Å2-0 Å2
3----3.3 Å2
Refinement stepCycle: 1 / Resolution: 2.53→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 3 4 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191365
X-RAY DIFFRACTIONr_bond_other_d0.0030.021317
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9181854
X-RAY DIFFRACTIONr_angle_other_deg0.9732998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35123.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7451513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02326
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_it3.2376.217674
X-RAY DIFFRACTIONr_mcbond_other3.2386.214673
X-RAY DIFFRACTIONr_mcangle_it4.9469.318839
X-RAY DIFFRACTIONr_mcangle_other4.9449.32840
X-RAY DIFFRACTIONr_scbond_it4.0196.846690
X-RAY DIFFRACTIONr_scbond_other4.0166.847691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.52310.0561016
X-RAY DIFFRACTIONr_long_range_B_refined9.30250.0851490
X-RAY DIFFRACTIONr_long_range_B_other9.29950.1031491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4187 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.533→2.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 36 -
Rwork0.43 412 -
obs--94.51 %
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)
13.50531.2121-1.1567.12281.16935.68560.0497-0.18840.1575-0.1755-0.11120.09880.1609-0.22470.06150.0591-0.0159-0.0720.03530.02420.27952.254-27.39-11.485
25.2172.591-1.98263.7135-1.59847.39240.2916-0.6736-0.1313-0.0572-0.2422-0.5665-0.57480.6758-0.04940.1621-0.07810.02250.1208-0.01890.452117.476-13.022-17.011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A206 - 291
2X-RAY DIFFRACTION2B209 - 292

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