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- PDB-4u9l: Structure of a membrane protein -

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Basic information

Entry
Database: PDB / ID: 4u9l
TitleStructure of a membrane protein
ComponentsMagnesium transporter MgtE
KeywordsMETAL TRANSPORT / channel / magnesium
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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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
DepositionAug 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
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_oper_list.symmetry_operation
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)40,4498
Polymers38,6422
Non-polymers1,8076
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-50 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.529, 70.165, 102.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Magnesium transporter MgtE


Mass: 19321.074 Da / Num. of mol.: 2 / Fragment: UNP residues 271-449
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: PEG600, Tris, Mg-formate, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21294 / % possible obs: 94.8 % / Redundancy: 2.6 % / Net I/σ(I): 9.62

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.3_1479) / Classification: refinement
RefinementResolution: 2.3→41.424 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 999 5.01 %
Rwork0.2244 --
obs0.2264 19947 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 67 39 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032773
X-RAY DIFFRACTIONf_angle_d0.7343781
X-RAY DIFFRACTIONf_dihedral_angle_d15.64966
X-RAY DIFFRACTIONf_chiral_restr0.023490
X-RAY DIFFRACTIONf_plane_restr0.004445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.37141440.33072722X-RAY DIFFRACTION99
2.4213-2.57290.34131430.29992730X-RAY DIFFRACTION99
2.5729-2.77160.32171440.27482731X-RAY DIFFRACTION99
2.7716-3.05040.30151440.23482751X-RAY DIFFRACTION99
3.0504-3.49160.24591450.21932733X-RAY DIFFRACTION98
3.4916-4.39830.21491430.20072727X-RAY DIFFRACTION97
4.3983-41.43020.24891360.19332554X-RAY DIFFRACTION94
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)
11.22410.8106-0.15742.08250.09641.5931-0.0096-0.2740.0986-0.09150.0756-0.08570.19030.62070.02210.40050.01860.01750.36060.03830.348634.66396.7622-2.3305
20.70880.60660.24420.87630.26351.23540.05490.0127-0.0097-0.05690.06270.15660.0636-0.30390.00020.23880.01530.0190.33560.00020.298313.04861.8048-3.2305
31.70040.65870.71381.3719-0.29380.56690.1287-0.02010.2865-0.00530.15370.0962-0.4898-0.19870.00240.42870.00490.04920.29090.04870.300120.3337.29741.1258
40.1064-0.0309-0.03740.00920.00970.0121-0.3812-0.22440.7476-0.37360.70020.2737-0.4387-0.73120.00190.6639-0.1968-0.14260.68950.13150.56475.15740.3436-20.0502
51.08720.36420.25721.0415-0.37251.1520.3185-0.1145-0.4645-0.00750.0532-0.18970.842-0.22980.02940.368-0.05050.0110.3802-0.01440.312518.4191-8.25942.4469
61.14-0.5395-0.2081.2211-0.34060.23070.60230.20730.2114-0.33530.1117-0.3151-0.6930.06010.01610.40450.02620.00770.3138-0.01490.326433.2566-1.2241-6.6644
71.6783-0.4433-0.461.2639-0.6160.80630.2313-0.1038-0.25060.0718-0.166-0.22720.1650.11560.00010.2862-0.0102-0.0150.28260.02560.289737.438-4.1186-2.3583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 271 through 312 )
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 414 )
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 449 )
4X-RAY DIFFRACTION4chain 'B' and (resid 271 through 277 )
5X-RAY DIFFRACTION5chain 'B' and (resid 278 through 312 )
6X-RAY DIFFRACTION6chain 'B' and (resid 313 through 348 )
7X-RAY DIFFRACTION7chain 'B' and (resid 349 through 448 )

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