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- PDB-4egw: The structure of the soluble domain of CorA from Methanocaldococc... -

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Basic information

Entry
Database: PDB / ID: 4egw
TitleThe structure of the soluble domain of CorA from Methanocaldococcus jannaschii
ComponentsMagnesium transport protein CorA
KeywordsMETAL TRANSPORT / magnesium transporter / magnesium binding / CORA
Function / homology
Function and homology information


cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / 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
1,4-BUTANEDIOL / HEXANE-1,6-DIOL / S-1,2-PROPANEDIOL / Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.5 Å
AuthorsGuskov, A. / Nordin, N. / Reynaud, A. / Engman, H. / Lundback, A.-K. / Jong, A.J.O. / Cornvik, T. / Phua, T. / Eshaghi, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA
Authors: Guskov, A. / Nordin, N. / Reynaud, A. / Engman, H. / Lundback, A.K. / Jong, A.J. / Cornvik, T. / Phua, T. / Eshaghi, S.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,70134
Polymers65,7902
Non-polymers2,91132
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.290, 68.290, 241.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Magnesium transport protein CorA


Mass: 32894.984 Da / Num. of mol.: 2 / Fragment: Soluble domain, UNP RESIDUES 1-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: corA, MJ1033 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58439

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Non-polymers , 5 types, 128 molecules

#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 8000, HEPES-MOPS, Alcohol mix, pH 7.5, 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: RAYONIX MX300HE / 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
Reflection twinOperator: k,h,-l / Fraction: 0.5
ReflectionResolution: 2.5→50 Å / Num. obs: 21977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.61 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD, molecular replacement / Resolution: 2.5→47.692 Å / σ(F): 2.01 / Phase error: 20.45 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 1099 5 %RANDOM
Rwork0.153 ---
obs0.1531 21977 99.86 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.293 Å2 / ksol: 0.37 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→47.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 193 96 4413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074373
X-RAY DIFFRACTIONf_angle_d1.3435829
X-RAY DIFFRACTIONf_dihedral_angle_d21.4521722
X-RAY DIFFRACTIONf_chiral_restr0.084677
X-RAY DIFFRACTIONf_plane_restr0.005707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5011-2.6150.26831380.2079261194
2.615-2.75280.22461370.1951259695
2.7528-2.92520.21891360.1855260395
2.9252-3.1510.211370.1663259095
3.151-3.4680.18891370.1505261695
3.468-3.96950.20691380.1345261695
3.9695-4.99990.15981370.119260595
4.9999-42.29210.20351390.1571262695
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)
13.6006-1.4136-0.76363.10010.31673.21590.0070.1513-0.6322-0.32780.2435-0.12170.90580.2772-0.18930.5595-0.04630.01350.2764-0.19630.641720.7166-41.8525-12.6917
21.17382.20870.32685.01830.28122.0465-0.0882-0.2038-0.43520.06670.0270.10460.2484-0.13490.02580.2194-0.09370.09080.1734-0.04890.629123.0957-33.1505-2.3745
37.4089-2.88022.41093.88120.09644.03880.37151.4215-0.7678-1.1292-0.1931-0.15120.4250.8881-0.17220.8504-0.13060.16880.5643-0.18060.651229.3458-34.8714-20.9801
40.9958-0.2011-0.17013.20580.70671.5563-0.0763-0.14780.1717-0.09970.06980.0251-0.20640.02470.00920.1869-0.03320.02070.0856-0.16250.582529.1383-12.3774-8.3838
51.05391.192-0.55842.30520.75632.3076-0.089-0.25510.4702-0.36550.1582-0.3762-0.55810.66740.08350.4069-0.208-0.10640.53470.0230.756249.21782.4366-24.7521
61.70970.66230.31822.33160.11782.2473-0.29790.30860.1872-0.19360.1283-0.0416-0.45160.42890.10270.2986-0.13510.00140.3575-0.07770.689540.9277-2.5841-36.2326
72.18870.4115-0.59182.0256-0.06151.94870.0771-0.3494-0.05120.0685-0.1484-0.22980.111-0.03480.07560.1891-0.032-0.02930.2769-0.14020.476330.3153-14.5558-27.8229
82.49121.26991.73491.7341-0.16872.8682-0.01930.0149-0.4122-0.144-0.0769-0.2790.2783-0.33440.13270.2867-0.05970.030.3049-0.11570.57525.0696-22.9032-31.9525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:37)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 38:109)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 110:133)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 134:250)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 1:28)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 29:109)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 110:210)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 211:250)

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