[English] 日本語
Yorodumi
- PDB-1s4s: Reaction Intermediate in the Photocycle of PYP, intermediate occu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s4s
TitleReaction Intermediate in the Photocycle of PYP, intermediate occupied between 100 micro-seconds to 5 milli-seconds
ComponentsPhotoactive yellow protein
KeywordsPHOTOSYNTHESIS / reaction intermediate
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchmidt, M. / Pahl, R. / Srajer, V. / Anderson, S. / Ren, Z. / Ihee, H. / Rajagopal, S. / Moffat, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data
Authors: Schmidt, M. / Pahl, R. / Srajer, V. / Anderson, S. / Ren, Z. / Ihee, H. / Rajagopal, S. / Moffat, K.
#1: Journal: Biophys.J. / Year: 2003
Title: Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data
Authors: Schmidt, M. / Rajagopal, S. / Ren, Z. / Moffat, K.
History
DepositionJan 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,8891
Non-polymers1641
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.900, 66.900, 40.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13888.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammoniumsulphate, Potassium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22881
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B11.0-1.5
SYNCHROTRONAPS 14-ID-B21.0-1.5
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 1, 2000
ADSC QUANTUM 42CCDDec 1, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
ReflectionResolution: 1.9→40 Å / Num. all: 8326 / Num. obs: 8326 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

-
Processing

Software
NameClassification
KB_SCANdata collection
LaueViewdata reduction
SVD4TXdata reduction
XTALVIEWrefinement
CNSrefinement
KB_SCANdata reduction
LaueViewdata scaling
SVD4TXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2phy

2phy


Resolution: 1.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residue 69 consits of Cys69 and the attached chromophore hydroxy-cinnamic acid. Dihedral of atoms O1 (carbonyl oxygen of chromophore), C1, C2 and C3 was inititally restrained to 0 deg (cis ...Details: Residue 69 consits of Cys69 and the attached chromophore hydroxy-cinnamic acid. Dihedral of atoms O1 (carbonyl oxygen of chromophore), C1, C2 and C3 was inititally restrained to 0 deg (cis planar). The restraint was reset to zero in the last cycle, the angle refined to 22 deg.
RfactorNum. reflection% reflection
Rfree0.2892 457 5 %
Rwork0.2446 --
obs0.2446 8326 -
all-8326 -
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 11 89 1166

+
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