[English] 日本語
Yorodumi
- PDB-5iip: Staphylococcus aureus OpuCA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iip
TitleStaphylococcus aureus OpuCA
ComponentsGlycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
KeywordsTRANSPORT PROTEIN / CBS domain / osmoprotection / c-di-AMP
Function / homology
Function and homology information


quaternary-amine-transporting ATPase / glycine betaine transport / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Glycine betaine transport ATP-binding subunit / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Glycine betaine transport ATP-binding subunit / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
: / ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTosi, T. / Campeotto, I. / Freemont, P.S. / Grundling, A.
CitationJournal: Sci.Signal. / Year: 2016
Title: The second messenger c-di-AMP inhibits the osmolyte uptake system OpuC in Staphylococcus aureus.
Authors: Schulte, L.E. / Schuster, C.F. / Tosi, T. / Campeotto, I. / Corrigan, R.M. / Freemont, P.S. / Grundling, A.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
B: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
C: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
D: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative


Theoretical massNumber of molelcules
Total (without water)87,4904
Polymers87,4904
Non-polymers00
Water27015
1
A: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
D: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative


Theoretical massNumber of molelcules
Total (without water)43,7452
Polymers43,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative
C: Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative


Theoretical massNumber of molelcules
Total (without water)43,7452
Polymers43,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.150, 88.260, 61.790
Angle α, β, γ (deg.)90.000, 114.790, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glycine betaine/carnitine/choline ABC transporter%2C ATP-binding protein%2C putative / Glycine/betaine ABC transporter ATP-binding protein


Mass: 21872.396 Da / Num. of mol.: 4 / Fragment: UNP residues 237-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: opuCA, CH51_13130, ERS445052_00945, RL02_02500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6GYR3, UniProt: A0A160MQL0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% Peg3350, 100 mM MES pH 6, 0.2M NH4Cl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→88.26 Å / Num. all: 17664 / Num. obs: 17664 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 3.2
Reflection shellRmerge(I) obs: 1.162

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kpb

3kpb


Resolution: 2.5→47.344 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.79
RfactorNum. reflection% reflection
Rfree0.2804 881 5 %
Rwork0.2444 --
obs0.2463 17618 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.02 Å2 / Biso mean: 49.7837 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 2.5→47.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 0 15 3732
Biso mean---44.12 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043760
X-RAY DIFFRACTIONf_angle_d0.7175089
X-RAY DIFFRACTIONf_chiral_restr0.029628
X-RAY DIFFRACTIONf_plane_restr0.002655
X-RAY DIFFRACTIONf_dihedral_angle_d15.5961427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.65670.39391210.286927722893100
2.6567-2.86180.30841480.278627852933100
2.8618-3.14970.32031950.284827392934100
3.1497-3.60530.32961250.25428252950100
3.6053-4.54170.24631500.211727882938100
4.5417-47.35250.24731420.23792828297099

+
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