[English] 日本語
Yorodumi
- PDB-4p1g: Crystal structure of the Bateman domain of murine magnesium trans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p1g
TitleCrystal structure of the Bateman domain of murine magnesium transporter CNNM2 bound to AMP
ComponentsMetal transporter CNNM2
KeywordsTRANSPORT PROTEIN / magnesium homeostasis / transport / hypomagnesemia / rare diseases / ACDP / Cyclin M
Function / homology
Function and homology information


magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / ATP binding / plasma membrane
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain ...Ancient conserved domain protein family / Ion transporter-like, CBS domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / RmlC-like jelly roll fold / Roll / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Metal transporter CNNM2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsCorral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. ...Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / Muller, D. / Martinez-Cruz, L.A.
CitationJournal: To Be Published
Title: Structural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4
Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / Muller, D. / Martinez-Cruz, L.A.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7432
Polymers17,3961
Non-polymers3471
Water0
1
A: Metal transporter CNNM2
hetero molecules

A: Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4864
Polymers34,7922
Non-polymers6942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.579, 105.579, 102.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / mACDP2 / Cyclin-M2


Mass: 17395.861 Da / Num. of mol.: 1 / Fragment: UNP residues 430-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnnm2, Acdp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TWN3
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na acetate pH 4.6, 3 M ammonium acetate, 10 mM AMP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→28.15 Å / Num. obs: 8072 / % possible obs: 99.6 % / Redundancy: 13.71 % / Biso Wilson estimate: 86.87 Å2 / Net I/σ(I): 53.58

-
Processing

Software
NameVersionClassification
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.7.3_928)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→28.15 Å / FOM work R set: 0.7828 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 901 10.02 %
Rwork0.2116 15182 -
obs0.2159 8072 99.63 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.962 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 179.98 Å2 / Biso mean: 90.97 Å2 / Biso min: 49.24 Å2
Baniso -1Baniso -2Baniso -3
1--3.8468 Å2-0 Å20 Å2
2---3.8468 Å20 Å2
3---7.6936 Å2
Refinement stepCycle: final / Resolution: 2.603→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 23 0 1236
Biso mean--89.48 --
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071259
X-RAY DIFFRACTIONf_angle_d1.1531707
X-RAY DIFFRACTIONf_chiral_restr0.073199
X-RAY DIFFRACTIONf_plane_restr0.004217
X-RAY DIFFRACTIONf_dihedral_angle_d15.209472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.603-2.67940.49411310.43151214134596
2.6794-2.76580.44111660.331712581424100
2.7658-2.86450.3851330.329212671400100
2.8645-2.97910.42751350.339212681403100
2.9791-3.11450.33261500.310512861436100
3.1145-3.27850.27281370.263412571394100
3.2785-3.48360.33571400.249912721412100
3.4836-3.7520.28071440.245612691413100
3.752-4.12850.22991350.192812671402100
4.1285-4.72350.19521320.160112831415100
4.7235-5.94190.21181410.178712571398100
5.9419-28.15140.22261460.185312841430100

+
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