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- PDB-4i0u: Improved structure of Thermotoga maritima CorA at 2.7 A resolution -

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Basic information

Entry
Database: PDB / ID: 4i0u
TitleImproved structure of Thermotoga maritima CorA at 2.7 A resolution
ComponentsMagnesium transport protein CorA
KeywordsMETAL TRANSPORT / magnesium/cobalt transport / MEMBRANE PROTEIN / CORA
Function / homology
Function and homology information


magnesium ion transmembrane transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / protein homooligomerization / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / 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 / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / 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 / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsNordin, N. / Guskov, A. / Phua, T. / Sahaf, N. / Xia, Y. / Lu, S.Y. / Eshaghi, H. / Eshaghi, S.
CitationJournal: Biochem.J. / Year: 2013
Title: Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport.
Authors: Nordin, N. / Guskov, A. / Phua, T. / Sahaf, N. / Xia, Y. / Lu, S.Y. / Eshaghi, H. / Eshaghi, S.
History
DepositionNov 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Mar 20, 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 / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
F: Magnesium transport protein CorA
G: Magnesium transport protein CorA
H: Magnesium transport protein CorA
I: Magnesium transport protein CorA
J: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,90672
Polymers414,98110
Non-polymers4,92562
Water4,342241
1
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)210,86139
Polymers207,4905
Non-polymers3,37034
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31640 Å2
ΔGint-358 kcal/mol
Surface area71520 Å2
MethodPISA
2
F: Magnesium transport protein CorA
G: Magnesium transport protein CorA
H: Magnesium transport protein CorA
I: Magnesium transport protein CorA
J: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,04533
Polymers207,4905
Non-polymers1,55428
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30510 Å2
ΔGint-320 kcal/mol
Surface area69740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.250, 151.500, 143.360
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJ

#1: Protein
Magnesium transport protein CorA


Mass: 41498.082 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: corA, TM_0561 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ31
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 300 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM MGCL2, 10% PEG 1500, 1% DDM, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.7→38.5 Å / Num. all: 121642 / Num. obs: 121600 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74.97 Å2
Reflection shellResolution: 2.7→2.7307 Å / % possible all: 77

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.7→38.305 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.56 / σ(F): 2.03 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 6079 5 %
Rwork0.2281 --
obs0.2312 121600 90.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.9318 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28551 0 294 241 29086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01129500
X-RAY DIFFRACTIONf_angle_d1.61839934
X-RAY DIFFRACTIONf_dihedral_angle_d17.47411296
X-RAY DIFFRACTIONf_chiral_restr0.1164550
X-RAY DIFFRACTIONf_plane_restr0.0084971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.40051690.33883201X-RAY DIFFRACTION77
2.7307-2.76280.40152080.34513947X-RAY DIFFRACTION92
2.7628-2.79650.42142060.35453920X-RAY DIFFRACTION93
2.7965-2.83190.38652070.35093944X-RAY DIFFRACTION93
2.8319-2.86910.41842110.33394001X-RAY DIFFRACTION94
2.8691-2.90840.33662070.32123944X-RAY DIFFRACTION93
2.9084-2.94990.41422070.33053929X-RAY DIFFRACTION94
2.9499-2.9940.38932090.32743966X-RAY DIFFRACTION93
2.994-3.04070.38612100.34053989X-RAY DIFFRACTION93
3.0407-3.09050.41912040.32333888X-RAY DIFFRACTION93
3.0905-3.14380.3452070.2983933X-RAY DIFFRACTION92
3.1438-3.2010.3782070.29343919X-RAY DIFFRACTION93
3.201-3.26250.51052010.41443843X-RAY DIFFRACTION90
3.2625-3.3290.53822050.48433900X-RAY DIFFRACTION92
3.329-3.40140.34312070.28793925X-RAY DIFFRACTION92
3.4014-3.48050.33532050.27053900X-RAY DIFFRACTION92
3.4805-3.56740.34082040.25513888X-RAY DIFFRACTION92
3.5674-3.66380.34472050.26083889X-RAY DIFFRACTION91
3.6638-3.77150.43462040.33633877X-RAY DIFFRACTION91
3.7715-3.89320.31962040.26043879X-RAY DIFFRACTION91
3.8932-4.03220.32352020.21813835X-RAY DIFFRACTION90
4.0322-4.19340.25922030.19833847X-RAY DIFFRACTION91
4.1934-4.3840.24832020.19073849X-RAY DIFFRACTION90
4.384-4.61480.23772020.17713824X-RAY DIFFRACTION89
4.6148-4.90340.2451990.17323785X-RAY DIFFRACTION89
4.9034-5.28110.23861990.18823783X-RAY DIFFRACTION88
5.2811-5.81090.28162000.19853790X-RAY DIFFRACTION89
5.8109-6.64790.25761970.19643754X-RAY DIFFRACTION88
6.6479-8.36130.22261980.18123761X-RAY DIFFRACTION87
8.3613-38.30880.22991900.18423611X-RAY DIFFRACTION83

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