[English] 日本語
Yorodumi
- PDB-4m8j: Crystal structure of CaiT R262E bound to gamma-butyrobetaine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m8j
TitleCrystal structure of CaiT R262E bound to gamma-butyrobetaine
ComponentsL-carnitine/gamma-butyrobetaine antiporter
KeywordsTRANSPORT PROTEIN / CaiT / LeuT fold / Carnitine/gamma-butyrobetaine antiporter / plasma membrane
Function / homology
Function and homology information


(R)-carnitine:4-(trimethylammonio)butanoate antiporter activity / 4-(trimethylammonio)butanoate transport / carnitine metabolic process / plasma membrane
Similarity search - Function
L-carnitine/gamma-butyrobetaine antiporter CaiT / BCCT transporter, conserved site / BCCT family of transporters signature. / BCCT transporter family / BCCT, betaine/carnitine/choline family transporter
Similarity search - Domain/homology
3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM / L-carnitine/gamma-butyrobetaine antiporter / :
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.294 Å
AuthorsKalayil, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Arginine oscillation explains Na+ independence in the substrate/product antiporter CaiT.
Authors: Kalayil, S. / Schulze, S. / Kuhlbrandt, W.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Sep 20, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-carnitine/gamma-butyrobetaine antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4312
Polymers56,2851
Non-polymers1461
Water181
1
A: L-carnitine/gamma-butyrobetaine antiporter
hetero molecules

A: L-carnitine/gamma-butyrobetaine antiporter
hetero molecules

A: L-carnitine/gamma-butyrobetaine antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,2946
Polymers168,8563
Non-polymers4393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area4360 Å2
ΔGint-42 kcal/mol
Surface area54220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.075, 129.075, 160.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein L-carnitine/gamma-butyrobetaine antiporter / CaiT / carnitine transporter


Mass: 56285.285 Da / Num. of mol.: 1 / Mutation: T176V, R262E, E443D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: caiT, HMPREF0693_2800 / Production host: Escherichia coli (E. coli) / References: UniProt: C2LLR0, UniProt: B4EY22*PLUS
#2: Chemical ChemComp-NM2 / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 19% PEG400, 50 mM calcium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97947 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.29→45.9 Å / Num. all: 15204 / Num. obs: 15128 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.289 / Net I/σ(I): 5.6
Reflection shellResolution: 3.29→3.55 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.093 / Mean I/σ(I) obs: 2 / Num. unique all: 3065 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WSW

2wsw


Resolution: 3.294→45.884 Å / SU ML: 0.4 / σ(F): 1.97 / Phase error: 27.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 750 5.01 %RANDOM
Rwork0.2359 ---
all0.241 15098 --
obs0.2369 14980 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.294→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 10 1 3885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034030
X-RAY DIFFRACTIONf_angle_d0.85515
X-RAY DIFFRACTIONf_dihedral_angle_d15.261357
X-RAY DIFFRACTIONf_chiral_restr0.052628
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.294-3.54790.30471540.28792751X-RAY DIFFRACTION97
3.5479-3.90480.321560.26852855X-RAY DIFFRACTION100
3.9048-4.46940.25071530.21542881X-RAY DIFFRACTION100
4.4694-5.62930.24271390.2342877X-RAY DIFFRACTION100
5.6293-45.88850.23111480.2242866X-RAY DIFFRACTION100

+
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