[English] 日本語
Yorodumi
- PDB-7jr5: Real Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jr5
TitleReal Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / phytochrome / photosensory core domain / time-resolved serial femtosecond crystallography / nanosecond / red/far-red / Z to E isomerization
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
BENZAMIDINE / Chem-VHG / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSchmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Structure / Year: 2021
Title: High-resolution crystal structures of transient intermediates in the phytochrome photocycle.
Authors: Carrillo, M. / Pandey, S. / Sanchez, J. / Noda, M. / Poudyal, I. / Aldama, L. / Malla, T.N. / Claesson, E. / Wahlgren, W.Y. / Feliz, D. / Srajer, V. / Maj, M. / Castillon, L. / Iwata, S. / ...Authors: Carrillo, M. / Pandey, S. / Sanchez, J. / Noda, M. / Poudyal, I. / Aldama, L. / Malla, T.N. / Claesson, E. / Wahlgren, W.Y. / Feliz, D. / Srajer, V. / Maj, M. / Castillon, L. / Iwata, S. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Tono, K. / Owada, S. / Westenhoff, S. / Stojkovic, E.A. / Schmidt, M.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9435
Polymers105,6452
Non-polymers1,2983
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-12 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.690, 83.400, 86.870
Angle α, β, γ (deg.)90.00, 107.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Photoreceptor-histidine kinase BphP


Mass: 52822.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (strain DW4/3-1) (bacteria)
Strain: DW4/3-1 / Gene: STIAU_8420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09E27
#2: Chemical ChemComp-VHG / 3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-5-[[(3~{S})-4-ethyl-3-methyl-2-oxidanylidene-1,3-dihydropyrrol-5-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 7
Details: SaBphP2 (60 mg/mL) was mixed 3:2 with a solution containing 0.17 M Ammonium-acetate, 85 mmol/L sodium citrate, pH 6.5, 25.5 % PEG 4000, 15% glycerol, 3 % benzamidine hydrochloride.

-
Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.38 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 18, 2018
RadiationMonochromator: no / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 38486 / % possible obs: 100 % / Redundancy: 543 % / CC1/2: 0.96 / R split: 0.094 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 158 % / Num. unique obs: 3035 / R split: 1.78 / % possible all: 100
Serial crystallography measurementFocal spot size: 5 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 8.9 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: viscous jet / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: nuclear grade grease / Flow rate: 4 µL/min / Injector diameter: 100 µm / Injector temperature: 289 K / Jet diameter: 100 µm / Power by: HPLC / Preparation: folding with grease

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6PTQ

6ptq


Resolution: 2.4→19.97 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.88 / SU B: 18.591 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R: 0.926 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34146 1799 4.7 %RANDOM
Rwork0.31275 ---
obs0.31412 36327 85.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20.17 Å2
2---0.2 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 96 7511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137730
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177352
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.68310566
X-RAY DIFFRACTIONr_angle_other_deg1.2291.58916905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0595972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24919.95399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.731151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5511580
X-RAY DIFFRACTIONr_chiral_restr0.2710.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028784
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021660
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_it1.6892.5493876
X-RAY DIFFRACTIONr_mcbond_other1.6892.553875
X-RAY DIFFRACTIONr_mcangle_it2.6953.8244849
X-RAY DIFFRACTIONr_mcangle_other2.6953.8234850
X-RAY DIFFRACTIONr_scbond_it1.3152.6223854
X-RAY DIFFRACTIONr_scbond_other1.3152.6223855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.13.915717
X-RAY DIFFRACTIONr_long_range_B_refined5.08631.3239457
X-RAY DIFFRACTIONr_long_range_B_other5.08431.3329453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.585 99 -
Rwork0.464 2091 -
obs--67.26 %

+
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