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- PDB-4ev6: The complete structure of CorA magnesium transporter from Methano... -

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Basic information

Entry
Database: PDB / ID: 4ev6
TitleThe complete structure of CorA magnesium transporter from Methanocaldococcus jannaschii
ComponentsMagnesium transport protein CorA
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / CORA / MAGNESIUM / ION TRANSPORTER
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
Cobalt/magnesium transport protein CorA
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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_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 / _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_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
C: Magnesium transport protein CorA
D: Magnesium transport protein CorA
E: Magnesium transport protein CorA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,45745
Polymers198,7075
Non-polymers4,75040
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29650 Å2
ΔGint-479 kcal/mol
Surface area71930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.110, 124.830, 111.880
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Magnesium transport protein CorA


Mass: 39741.316 Da / Num. of mol.: 5
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
#2: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 8000, HEPES-NAOH, 60mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 46906 / Num. obs: 46822 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 82.14 Å2
Reflection shellResolution: 3.2→3.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EGW

4egw


Resolution: 3.2→49.44 Å / SU ML: 1.12 / σ(F): 1.99 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 2343 5 %random
Rwork0.2054 ---
obs0.2092 46822 99.85 %-
all-46906 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.635 Å2 / ksol: 0.229 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8471 Å20 Å2-0.9486 Å2
2--1.0911 Å20 Å2
3----1.9382 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12975 0 255 200 13430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113454
X-RAY DIFFRACTIONf_angle_d1.50618173
X-RAY DIFFRACTIONf_dihedral_angle_d19.4035114
X-RAY DIFFRACTIONf_chiral_restr0.1092148
X-RAY DIFFRACTIONf_plane_restr0.0052196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.26530.41441360.331125902726100
3.2653-3.33630.39591390.284726352774100
3.3363-3.41390.3151360.249525752711100
3.4139-3.49920.31551380.236726192757100
3.4992-3.59380.32381370.242426032740100
3.5938-3.69950.37911370.263726112748100
3.6995-3.81890.28291370.219225992736100
3.8189-3.95540.29111380.183126172755100
3.9554-4.11360.23951360.177926032739100
4.1136-4.30080.28111400.162126472787100
4.3008-4.52740.27111360.151825832719100
4.5274-4.81080.2251380.139426282766100
4.8108-5.18190.21511380.148926092747100
5.1819-5.70270.29131380.195826182756100
5.7027-6.52620.28521390.218426512790100
6.5262-8.21630.27361380.184526282766100
8.2163-49.4460.26951420.24572663280599
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)
16.13831.25030.17185.4617-0.04415.9833-0.14830.2022-0.27880.02960.3249-0.99210.27391.004-0.07710.3996-0.0888-0.04870.444-0.09190.35929.4817-5.6601-10.4226
20.90820.408-1.96560.6043-0.96974.86470.0504-0.1152-0.09790.2274-0.0523-0.03160.0640.17160.00040.41430.013-0.11410.346-0.03440.2661-16.7785-16.459323.9711
34.16680.6268-0.32174.2108-0.28171.9472-0.21420.29761.076-0.0291-0.11450.6818-1.2647-0.29660.04571.1050.1113-0.45010.3907-0.02430.7602-22.015826.2777-9.4612
40.6580.90730.44161.55631.00050.7986-1.3911-0.00611.2177-0.7879-0.4088-1.4472-2.03061.13871.56042.1392-0.2727-1.00760.91820.36541.8854-5.037723.1598-18.3512
53.81840.4664-0.79325.8088-0.18913.9043-0.2439-0.37740.02270.5410.1510.0342-0.17140.35090.02780.30150.01140.00560.0924-0.01520.3324-17.54418.55842.9212
60.5324-0.1337-0.52651.292-2.83047.571-0.1752-0.2294-0.1305-0.12920.0494-0.10020.94930.44140.12060.78370.0149-0.09820.3849-0.03320.378-16.8815-10.672938.6994
73.3244-0.41931.05724.128-1.32640.6844-0.1995-0.15020.0414-0.48890.10421.3144-0.666-0.9559-0.2350.69860.3984-0.2061.286-0.09690.6897-59.09392.2547-10.6351
83.0569-0.44440.37723.1869-0.17753.2411-0.2582-0.13390.4191-0.05360.07520.3098-0.8341-0.3340.12120.37480.2763-0.12750.44410.00160.2048-44.44635.4613-2.4553
91.2013-0.54072.54120.824-1.07177.6988-0.02010.3130.1246-0.3443-0.0652-0.07590.0240.0651-0.04770.37090.07540.09980.4492-0.04990.2038-30.109-0.053714.338
106.8958-0.2653-1.22133.9056-0.22765.89790.11060.0192-0.0615-0.3503-0.11-0.17490.17050.3543-0.00690.8327-0.0838-0.20950.5510.1220.3442-14.0389-3.229165.3966
114.37091.8718-0.04054.32961.02333.2496-0.00940.1496-0.2458-0.4427-0.27191.1660.2432-0.8640.24060.4995-0.3855-0.29270.5454-0.2080.8075-52.529-33.3982-11.2035
120.5075-0.04790.66681.12061.96767.93320.0089-0.117-0.02530.1438-0.0580.0682-0.0943-0.9710.08610.431-0.0058-0.08370.41930.0820.3017-37.2377-10.620823.3514
132.5554-1.56890.23253.8889-1.2052.75470.13080.1183-0.3989-0.34950.00650.25170.67960.0323-0.09020.39230.2344-0.16140.04340.04020.1481-7.4363-41.3963-10.2128
141.9851-0.58380.10732.84010.99454.2050.0826-0.273-0.14420.248-0.00260.26760.4084-0.58530.13670.3326-0.1026-0.05850.16120.0060.0766-22.7388-28.43542.1209
152.9575-0.11210.23841.3084-0.38761.8621-0.17320.10930.2169-0.29860.05640.2-0.2692-0.66450.1310.530.1288-0.20550.49840.01150.1796-38.7351-9.929660.0656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:131)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 132:317)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 4:120)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 121:131)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 132:210)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 211:317)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 4:92)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 93:210)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 211:266)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 267:317)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 4:130)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 131:317)
13X-RAY DIFFRACTION13CHAIN E AND (RESSEQ 1:131)
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 132:249)
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 250:317)

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