[English] 日本語
Yorodumi
- PDB-3g6o: Crystal structure of P. aeruginosa bacteriophytochrome PaBphP pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g6o
TitleCrystal structure of P. aeruginosa bacteriophytochrome PaBphP photosensory core domain mutant Q188L
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / alpha/beta structure / PAS domain / Chromophore / Kinase / Phosphoprotein / Photoreceptor protein / Receptor / Sensory transduction / Transferase
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein 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 / Bacteriophytochrome
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsYang, X. / Kuk, J. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome
Authors: Yang, X. / Kuk, J. / Moffat, K.
History
DepositionFeb 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7824
Polymers113,6172
Non-polymers1,1652
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-46 kcal/mol
Surface area42800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.786, 109.786, 189.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 56808.262 Da / Num. of mol.: 2 / Fragment: PHOTOSENSORY CORE DOMAIN / Mutation: Q188L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWR3, histidine kinase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.5% PEG4000(w/v), 0.01M sodium acetate, 10mg/ml protein in dark, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.981
DetectorType: MAR CCD 165 MM 315 / Detector: CCD / Date: Jul 21, 2008
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 28350 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.85→3 Å / Redundancy: 7.3 % / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BioCARSuControldata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.85→42.47 Å / SU ML: 0.36
Isotropic thermal model: each chain was treated as an independent TLS group
σ(F): 1.34 / Phase error: 38.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1281 5.14 %
Rwork0.229 --
obs0.232 24940 82.8 %
all-28493 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.55 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.0301 Å20 Å2-0 Å2
2--7.0301 Å20 Å2
3----14.0601 Å2
Refinement stepCycle: LAST / Resolution: 2.85→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7338 0 172 2 7512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067699
X-RAY DIFFRACTIONf_angle_d1.25610481
X-RAY DIFFRACTIONf_dihedral_angle_d18.0142803
X-RAY DIFFRACTIONf_chiral_restr0.0741125
X-RAY DIFFRACTIONf_plane_restr0.0051362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.96410.4316710.34371165X-RAY DIFFRACTION37
2.9641-3.0990.3896710.31641698X-RAY DIFFRACTION54
3.099-3.26230.35131240.29932216X-RAY DIFFRACTION70
3.2623-3.46660.38971280.28462800X-RAY DIFFRACTION88
3.4666-3.73410.3371800.25563153X-RAY DIFFRACTION100
3.7341-4.10960.27681710.23923169X-RAY DIFFRACTION100
4.1096-4.70360.27471690.19383167X-RAY DIFFRACTION100
4.7036-5.92350.29371750.20693188X-RAY DIFFRACTION100
5.9235-42.47770.25791920.20053103X-RAY DIFFRACTION97
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)
12.2118-0.0745-1.3111.01040.10691.6629-0.0895-0.83840.67560.21110.268-0.236-0.2220.7255-0.21210.4168-0.1403-0.13460.6308-0.32320.594549.212657.771214.5137
22.1502-1.00660.97241.3677-1.24981.09990.52510.4041-0.4262-0.5125-0.22640.39770.79160.1414-0.2930.77780.0159-0.19070.3818-0.23470.56929.424623.408617.2817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 1
2X-RAY DIFFRACTION2chain BB6 - 2

+
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