[English] 日本語
Yorodumi
- PDB-4ev6: The complete structure of CorA magnesium transporter from Methano... -

+
Open data


ID or keywords:

Loading...

-
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 / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / 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 / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more