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- PDB-4wib: Crystal structure of Magnesium transporter MgtE -

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Basic information

Entry
Database: PDB / ID: 4wib
TitleCrystal structure of Magnesium transporter MgtE
ComponentsMagnesium transporter MgtE
KeywordsMETAL TRANSPORT / channel / magnesium / transporter
Function / homology
Function and homology information


magnesium ion transport / magnesium ion transmembrane transporter activity / magnesium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
SLC41 divalent cation transporters, integral membrane domain / MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Domain in cystathionine beta-synthase and other proteins. ...SLC41 divalent cation transporters, integral membrane domain / MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Domain in cystathionine beta-synthase and other proteins. / Tetracycline Repressor; domain 2 / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsTakeda, H. / Hattori, M. / Nishizawa, T. / Yamashita, K. / Shah, S.T.A. / Caffrey, M. / Maturana, A.D. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE
Authors: Takeda, H. / Hattori, M. / Nishizawa, T. / Yamashita, K. / Shah, S.T. / Caffrey, M. / Maturana, A.D. / Ishitani, R. / Nureki, O.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy / Structure summary
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 20, 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_struct_conn_angle / refine_hist / struct_conn
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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium transporter MgtE
B: Magnesium transporter MgtE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5804
Polymers38,5002
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-60 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.120, 70.380, 103.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsasymmetric unit contains two biological units

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Components

#1: Protein Magnesium transporter MgtE


Mass: 19249.996 Da / Num. of mol.: 2 / Fragment: UNP residues 271-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SMG8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG400, CaCl2, NaSCN, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.97914 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 7850 / % possible obs: 90.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 77.52 Å2 / Net I/σ(I): 1.67

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.3_1479)refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.2→43.083 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 393 5.01 %
Rwork0.2405 7457 -
obs0.2419 7850 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.75 Å2 / Biso mean: 67.0027 Å2 / Biso min: 33.77 Å2
Refinement stepCycle: final / Resolution: 3.2→43.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 2 0 2610
Biso mean--72.73 --
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042660
X-RAY DIFFRACTIONf_angle_d1.0113654
X-RAY DIFFRACTIONf_chiral_restr0.035481
X-RAY DIFFRACTIONf_plane_restr0.005437
X-RAY DIFFRACTIONf_dihedral_angle_d16.142884
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.66290.35171310.329224972628100
3.6629-4.6140.27051210.23892295241690
4.614-43.08690.22751410.208526652806100
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)
11.84131.00291.35991.6181-0.111.62790.057-0.1854-0.0745-0.1476-0.1910.0828-0.2821-0.62060.05740.50590.0279-0.08750.3605-0.02760.42823.529-3.764-2.5179
21.1866-0.82620.01641.8509-1.2011.05710.0688-0.0747-0.2002-0.2976-0.1599-0.0458-0.04530.74660.0740.5838-0.19670.01490.5914-0.02770.55122.8287-1.0987-6.0814
32.4855-0.0275-2.61391.73370.62872.9875-0.1318-0.1006-0.09790.3822-0.04930.19570.29450.01560.15660.48310.0673-0.07830.4623-0.01390.529114.8373-5.63270.2803
42.0822-0.4485-0.37270.6620.50071.8450.0801-0.03570.1863-0.1391-0.10720.1171-0.3125-0.1770.02670.6235-0.02060.01080.4411-0.01420.4289-0.24933.4454-3.6877
53.83380.3766-2.23142.6532-0.6526.91540.44640.42150.3271-0.14250.2171-0.2145-1.11690.0834-0.3680.9864-0.07130.11540.5001-0.08770.7698-0.3257.87970.316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 271 through 343 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 381 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 448 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 271 through 415 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 416 through 448 )B0

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