[English] 日本語
Yorodumi
- PDB-6p5d: Photoactive Yellow Protein PYP 30ps -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p5d
TitlePhotoactive Yellow Protein PYP 30ps
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PYP / 10ps
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
Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPandey, S. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Nat.Methods / Year: 2020
Title: Time-resolved serial femtosecond crystallography at the European XFEL.
Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / ...Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / Bondar, V. / Echelmeier, A. / Doppler, D. / Emons, M. / Frank, M. / Fromme, R. / Gevorkov, Y. / Giovanetti, G. / Jiang, M. / Kim, D. / Kim, Y. / Kirkwood, H. / Klimovskaia, A. / Knoska, J. / Koua, F.H.M. / Letrun, R. / Lisova, S. / Maia, L. / Mazalova, V. / Meza, D. / Michelat, T. / Ourmazd, A. / Palmer, G. / Ramilli, M. / Schubert, R. / Schwander, P. / Silenzi, A. / Sztuk-Dambietz, J. / Tolstikova, A. / Chapman, H.N. / Ros, A. / Barty, A. / Fromme, P. / Mancuso, A.P. / Schmidt, M.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photoactive yellow protein


Theoretical massNumber of molelcules
Total (without water)14,0351
Polymers14,0351
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
MethodPISA
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: 14034.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: small tubes / Details: Sodium Malonate

-
Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.6→11.81 Å / Num. obs: 12318 / % possible obs: 93.27 % / Redundancy: 287.6 % / Net I/σ(I): 13.98
Reflection shellResolution: 1.6→1.641 Å / Num. unique obs: 811

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→11.81 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.177 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26651 620 4.8 %RANDOM
Rwork0.22057 ---
obs0.22275 12318 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 7.007 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.6→11.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 92 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021044
X-RAY DIFFRACTIONr_bond_other_d0.0010.02967
X-RAY DIFFRACTIONr_angle_refined_deg2.5431.9621410
X-RAY DIFFRACTIONr_angle_other_deg1.11532237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9875124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15725.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42915181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.303153
X-RAY DIFFRACTIONr_chiral_restr0.1530.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4570.701499
X-RAY DIFFRACTIONr_mcbond_other0.4570.701498
X-RAY DIFFRACTIONr_mcangle_it0.6831.05622
X-RAY DIFFRACTIONr_mcangle_other0.6831.05623
X-RAY DIFFRACTIONr_scbond_it0.3260.678545
X-RAY DIFFRACTIONr_scbond_other0.3260.678545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5021.014788
X-RAY DIFFRACTIONr_long_range_B_refined1.8535.461218
X-RAY DIFFRACTIONr_long_range_B_other1.5595.4131194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 36 -
Rwork0.348 811 -
obs--85.38 %

+
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