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- PDB-5n77: Crystal structure of the cytosolic domain of the CorA magnesium c... -

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Basic information

Entry
Database: PDB / ID: 5n77
TitleCrystal structure of the cytosolic domain of the CorA magnesium channel from Escherichia coli in complex with magnesium
ComponentsMagnesium transport protein CorA
KeywordsTRANSPORT PROTEIN / Homopentamer Complex Transport Membrane
Function / homology
Function and homology information


nickel cation transmembrane transport / nickel cation transmembrane transporter activity / magnesium ion transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / plasma membrane
Similarity search - Function
Magnesium/cobalt transport protein CorA / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Magnesium transport protein CorA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLerche, M. / Sandhu, H. / Flockner, L. / Hogbom, M. / Rapp, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Carl Tryggers stiftelse Sweden
Knut and Alice Wallenberg Foundation Sweden
Swedish Foundation for Strategic Research Sweden
CitationJournal: Structure / Year: 2017
Title: Structure and Cooperativity of the Cytosolic Domain of the CorA Mg(2+) Channel from Escherichia coli.
Authors: Lerche, M. / Sandhu, H. / Flockner, L. / Hogbom, M. / Rapp, M.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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.ptnr3_auth_asym_id / _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.value / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium transport protein CorA
B: Magnesium transport protein CorA
C: Magnesium transport protein CorA
D: Magnesium transport protein CorA
E: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,88315
Polymers149,3535
Non-polymers53110
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-106 kcal/mol
Surface area52860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.313, 117.453, 91.114
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12C
22A
13C
23B
14C
24E
15D
25A
16D
26B
17D
27E
18A
28B
19A
29E
110B
210E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010C1 - 258
2010D1 - 258
1020C1 - 258
2020A1 - 258
1030C1 - 258
2030B1 - 258
1040C1 - 258
2040E1 - 258
1050D1 - 258
2050A1 - 258
1060D1 - 258
2060B1 - 258
1070D1 - 258
2070E1 - 258
1080A1 - 258
2080B1 - 258
1090A1 - 258
2090E1 - 258
10100B1 - 258
20100E1 - 258

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Magnesium transport protein CorA


Mass: 29870.543 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: corA, b3816, JW3789 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABI4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20 mM MgCl2; 100 mM Glycine pH8.7; 8-18% PEG400; 0,5-2% TritonX-114.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→29.84 Å / Num. obs: 36878 / % possible obs: 99 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.746 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 36.054 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23591 1869 5.1 %RANDOM
Rwork0.19461 ---
obs0.19672 34990 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.456 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å21.35 Å2
2---2.07 Å20 Å2
3---2.99 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10387 0 31 115 10533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910598
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210066
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.96814287
X-RAY DIFFRACTIONr_angle_other_deg1.03323034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95351278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70424.328603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.136151915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.10715108
X-RAY DIFFRACTIONr_chiral_restr0.070.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212145
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022521
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_it3.0864.355133
X-RAY DIFFRACTIONr_mcbond_other3.0874.355132
X-RAY DIFFRACTIONr_mcangle_it5.0526.5246404
X-RAY DIFFRACTIONr_mcangle_other5.0526.5246405
X-RAY DIFFRACTIONr_scbond_it4.1874.8445465
X-RAY DIFFRACTIONr_scbond_other4.1874.8455466
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8197.077884
X-RAY DIFFRACTIONr_long_range_B_refined9.42233.68611550
X-RAY DIFFRACTIONr_long_range_B_other9.42233.69311551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C158830.07
12D158830.07
21C157650.07
22A157650.07
31C160410.05
32B160410.05
41C158960.06
42E158960.06
51D160790.06
52A160790.06
61D160610.06
62B160610.06
71D161250.05
72E161250.05
81A158860.07
82B158860.07
91A160630.06
92E160630.06
101B160010.06
102E160010.06
LS refinement shellResolution: 2.795→2.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 111 -
Rwork0.374 2252 -
obs--86.91 %
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)
12.05110.42281.05331.88940.33771.84120.13260.03-0.109-0.19590.0160.28430.2637-0.1201-0.14850.0711-0.0228-0.0550.0182-0.00930.2023-49.09630.0009-9.2676
21.95540.70630.06332.01950.00881.65580.1157-0.2347-0.29590.3566-0.01140.07350.4188-0.3212-0.10430.1733-0.07540.01040.09450.07820.1451-49.1476-4.016722.639
31.9994-0.77490.63471.5040.00081.89960.07770.1872-0.0591-0.3587-0.06630.1261-0.3044-0.202-0.01150.13730.0486-0.01130.060.00460.1061-48.732431.228-14.8641
41.8008-1.0664-0.62142.14790.51261.20130.1491-0.00170.1541-0.06120.04360.0906-0.2326-0.1874-0.19270.04750.0370.04460.03960.030.1295-49.08946.561812.9983
51.80880.1476-1.45631.2947-0.37052.27120.0864-0.1261-0.07470.40240.10420.1528-0.1355-0.1102-0.19060.12780.03050.04340.05990.060.0695-49.435824.621636.3318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 257
2X-RAY DIFFRACTION2D1 - 257
3X-RAY DIFFRACTION3A1 - 257
4X-RAY DIFFRACTION4B1 - 257
5X-RAY DIFFRACTION5E1 - 257

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