[English] 日本語
Yorodumi
- PDB-5ahz: Bromide-bound form of Halorhodopsin from Halobacterium salinarum ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ahz
TitleBromide-bound form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form
ComponentsHALORHODOPSIN
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / HALOPHILIC ARCHAEA / ARCHAEAL RHODOPSIN / LIGHT DRIVEN ION PUMP / RETINAL PROTEIN / ION TRANSMEMBRANE TRANSPORT
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / RETINAL / Halorhodopsin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsSchreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of Halorhodopsin from Halobacterium Salinarum in a New Crystal Form that Imposes Little Restraint on the E-F Loop.
Authors: Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H.
History
DepositionFeb 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Dec 14, 2016Group: Data collection
Revision 1.4May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6825
Polymers27,9461
Non-polymers7374
Water43224
1
A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules

A: HALORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,04715
Polymers83,8373
Non-polymers2,21012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area8650 Å2
ΔGint-72.7 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.040, 104.040, 138.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein HALORHODOPSIN


Mass: 27945.709 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-274
Source method: isolated from a genetically manipulated source
Details: IMINE BOND (SCHIFF BASE) BETWEEN NZ OF LYS242 AND C15 OF THE RETINAL LIGAND
Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: L33 / Production host: HALOBACTERIUM SALINARUM (Halophile) / Strain (production host): L33 / References: UniProt: B0R2U4
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsRETINAL (RET): RETINAL IS COVALENTLY LINKED TO LYS242 BY IMINE BOND
Sequence detailsAMINO ACIDS 1-19 ARE MISSING (CLEAVED SIGNAL PEPTIDE), C- TERMINAL HEXAHISTIDIN-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 % / Description: NONE
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: RESERVOIR SOLUTION: 100 MM CITRATE PH 8, 150 MM NABR, 2.3 M (NH4)2SO4. VAPOR DIFFUSION AT 296 K WITH DROP RATIO OF 1.2 TO 0.8 UL PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 7 MG/ML.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2013 / Details: PT COATED SI MIRROR
RadiationMonochromator: CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.45→42.8 Å / Num. obs: 10814 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 40.53 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.98 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: ISOMORPHOUS STRUCTURE OF CHLORIDE-BOUND HALORHODOPSIN, PDB ID 5AHY

5ahy


Resolution: 2.45→42.836 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 26.8 / Stereochemistry target values: ML
Details: RESIDUES 263-274 AS WELL AS THE C-TERMINAL HEXAHISTIDINE-TAG ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2398 528 4.9 %
Rwork0.1877 --
obs0.1903 10804 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.45→42.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 42 24 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091923
X-RAY DIFFRACTIONf_angle_d1.1522636
X-RAY DIFFRACTIONf_dihedral_angle_d13.564639
X-RAY DIFFRACTIONf_chiral_restr0.039329
X-RAY DIFFRACTIONf_plane_restr0.005313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.69660.31191230.21072537X-RAY DIFFRACTION100
2.6966-3.08670.26411380.19052533X-RAY DIFFRACTION100
3.0867-3.88850.2391300.17862557X-RAY DIFFRACTION100
3.8885-42.84210.21731370.18622649X-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