[English] 日本語
Yorodumi
- PDB-5i5l: The photosensory module (PAS-GAF-PHY) of the bacterial phytochrom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i5l
TitleThe photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A
ComponentsBacteriophytochrome protein
KeywordsSIGNALING PROTEIN / bilin protein / photoisomerization / parallel dimer
Function / homology
Function and homology information


red or far-red light photoreceptor activity / red, far-red light phototransduction / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
PHY 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. / GAF domain ...PHY 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. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS 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 / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNagano, S. / Scheerer, P. / Zubow, K. / Lamparter, T. / Krauss, N.
Funding support Germany, United Kingdom, 4items
OrganizationGrant numberCountry
German Research FoundationSFB498-B2 Germany
German Research FoundationSFB1078-B6 Germany
Queen Mary University of LondonPostgraduate Research Studentship United Kingdom
University of London, Central Research FundAR/CRF/B United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.
Authors: Nagano, S. / Scheerer, P. / Zubow, K. / Michael, N. / Inomata, K. / Lamparter, T. / Krau, N.
History
DepositionFeb 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
SupersessionJun 23, 2021ID: 4WKK
Revision 1.4Jun 23, 2021Group: Advisory / Derived calculations
Category: pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6055
Polymers54,7271
Non-polymers8784
Water41423
1
A: Bacteriophytochrome protein
hetero molecules

A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,21010
Polymers109,4542
Non-polymers1,7568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Unit cell
Length a, b, c (Å)173.019, 173.019, 78.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Bacteriophytochrome protein


Mass: 54726.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry ...Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry AAT99575 (NCBI). The respective numbering was used in a number of publications on this protein, and we did not change it in this entry for the sake of consistency with published work and because the true N-terminus has not yet been identified at the protein level
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu1990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7CY45

-
Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.7 Å3/Da / Density % sol: 54.5 % / Description: tetragonal column
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 16% PEG3350, 0.2 M CaCl2, 0.1 M Tris/HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.7→46.55 Å / Num. obs: 16105 / % possible obs: 96.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 62.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSQ

5hsq


Resolution: 2.7→46.55 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 33.382 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 1.363 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27901 830 5.2 %RANDOM
Rwork0.21566 ---
obs0.2187 15275 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.119 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 61 23 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193697
X-RAY DIFFRACTIONr_bond_other_d0.0020.023403
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9625040
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0027776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99123.576151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4011525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
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_it1.4325.2571918
X-RAY DIFFRACTIONr_mcbond_other1.4325.2531916
X-RAY DIFFRACTIONr_mcangle_it2.4717.8752391
X-RAY DIFFRACTIONr_mcangle_other2.4717.8782392
X-RAY DIFFRACTIONr_scbond_it1.4415.3171779
X-RAY DIFFRACTIONr_scbond_other1.445.3161779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3687.9252650
X-RAY DIFFRACTIONr_long_range_B_refined4.54462.0154083
X-RAY DIFFRACTIONr_long_range_B_other4.52262.0034080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 46 -
Rwork0.292 893 -
obs--78.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7669-1.114-0.23713.56160.23635.1103-0.0630.0629-0.2222-0.06020.1116-0.15450.51840.2159-0.04860.14280.10210.06850.10960.02870.1923-17.987-46.727-38.648
22.0667-1.7924-1.35463.16961.99421.3442-0.3548-0.1182-0.27080.58360.01340.41550.36040.08330.34130.18650.01610.05270.13830.02940.2643-29.112-33.908-19.563
35.6482-3.5996-2.34622.95332.20731.8968-0.09030.31060.15670.1248-0.21550.1754-0.0254-0.10120.30580.1466-0.0568-0.02410.0684-0.06170.3555-47.888-8.166-11.492
47.7127-3.0271-3.26872.63650.5811.72630.2638-0.0991-0.476-0.1224-0.40560.3398-0.10890.25180.14180.15840.0345-0.11860.2004-0.06720.4732-20.457-26.187-21.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 123
2X-RAY DIFFRACTION2A124 - 334
3X-RAY DIFFRACTION3A335 - 502
4X-RAY DIFFRACTION4A601

+
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://pdbjlvh1.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