[English] 日本語
Yorodumi
- PDB-1kou: Crystal Structure of the Photoactive Yellow Protein Reconstituted... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kou
TitleCrystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTOSYNTHESIS / photoreceptor
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
CAFFEIC ACID / N-BUTANE / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
Authorsvan Aalten, D.M.F. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.
Authors: van Aalten, D.M. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L.
History
DepositionDec 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOTOACTIVE YELLOW PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1273
Polymers13,8891
Non-polymers2382
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.582, 40.582, 117.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
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) / Gene: PYP / Plasmid: PHISP / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P16113
#2: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#3: Chemical ChemComp-NBU / N-BUTANE


Mass: 58.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.54 Å3/Da / Density % sol: 20.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
350 mMMES1reservoirpH6.5
2PEG2000 MME1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.16→15 Å / Num. obs: 36609 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.7
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3352 / % possible all: 89.4
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 333681 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 89.4 % / Num. unique obs: 3352 / Rmerge(I) obs: 0.546

-
Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHY

2phy


Resolution: 1.16→8 Å / Num. parameters: 9856 / Num. restraintsaints: 12084 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 1736 5 %RANDOM
Rwork0.1618 ---
obs0.1621 -92.3 %-
all-34756 --
Displacement parametersBiso mean: 20.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Num. disordered residues: 5 / Occupancy sum hydrogen: 862 / Occupancy sum non hydrogen: 1069
Refinement stepCycle: LAST / Resolution: 1.16→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 24 135 1102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0338
X-RAY DIFFRACTIONs_zero_chiral_vol0.14
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.124
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.096
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.162 / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.12

+
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