[English] 日本語
Yorodumi
- PDB-3c2w: Crystal structure of the photosensory core domain of P. aeruginos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c2w
TitleCrystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / Knot structure / 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 / phosphorelay sensor kinase activity / photoreceptor 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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, X. / Kuk, J. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.
Authors: Yang, X. / Kuk, J. / Moffat, K.
History
DepositionJan 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
E: Bacteriophytochrome
F: Bacteriophytochrome
G: Bacteriophytochrome
H: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,24716
Polymers454,5868
Non-polymers4,6618
Water54030
1
E: Bacteriophytochrome
F: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-58 kcal/mol
Surface area41810 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-51 kcal/mol
Surface area43080 Å2
MethodPISA
3
G: Bacteriophytochrome
H: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-54 kcal/mol
Surface area43220 Å2
MethodPISA
4
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-47 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.417, 164.255, 434.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56823.230 Da / Num. of mol.: 8 / Fragment: photosensory core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HWR3, histidine kinase
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.45M (NH4)H2PO4 0.1M Tris HCl 10mg/ml protein, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 150452 / Num. obs: 89068 / % possible obs: 59.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 70.12 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.4 / % possible all: 100

-
Processing

Software
NameClassification
HKL-3000data collection
SHARPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A partial model built from a mutant structure determined by MAD phasing

Resolution: 2.9→14.996 Å / SU ML: 0.4 / Isotropic thermal model: TLS / Phase error: 36.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 4371 5 %
Rwork0.2188 --
obs0.2221 87377 72.1 %
all-121194 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.335 Å2 / ksol: 0.259 e/Å3
Displacement parametersBiso mean: 126.92 Å2
Baniso -1Baniso -2Baniso -3
1-22.401 Å20 Å2-0 Å2
2--18.381 Å2-0 Å2
3----40.782 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30117 0 344 30 30491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531166
X-RAY DIFFRACTIONf_angle_d1.08942329
X-RAY DIFFRACTIONf_dihedral_angle_d17.55411424
X-RAY DIFFRACTIONf_chiral_restr0.0744622
X-RAY DIFFRACTIONf_plane_restr0.0045538
LS refinement shellResolution: 2.9→2.93 Å
RfactorNum. reflection% reflection
Rfree0.48 38 -
Rwork0.383 742 -
obs--20 %
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)
1-0.64530.37690.1370.4707-0.1321.55330.0724-0.0665-0.0044-0.02350.19680.0744-0.1084-0.0468-0.25580.2329-0.0123-0.05220.49950.11110.4376-17.854218.081898.2925
20.4068-0.0590.17860.8752-0.00310.674-0.0617-0.2259-0.2427-0.11030.23030.31880.1311-0.2608-0.17210.5097-0.2299-0.22320.69030.25810.7397-40.3775-7.621784.0241
30.3655-0.29140.12260.90160.93791.7505-0.0635-0.07050.0637-0.06850.1655-0.04510.0407-0.1238-0.08240.4811-0.0682-0.08080.4182-0.0310.4958-41.555860.422665.8867
40.00540.1715-0.07040.48670.09540.80580.2013-0.07980.01560.0582-0.03240.09320.1296-0.4352-0.14070.4859-0.2675-0.21110.8790.28810.6868-70.972237.475566.4169
50.67590.2762-0.0250.08470.43040.77370.03860.2575-0.0298-0.17930.12280.0869-0.36760.4935-0.06290.8486-0.2225-0.22190.92160.18010.6515-50.250660.808311.1766
60.56730.01110.19810.61310.23940.61870.23920.0065-0.0418-0.1827-0.17980.00480.0348-0.0742-0.0460.7091-0.0851-0.17660.53290.12260.4065-77.926338.32421.3324
70.81080.0667-0.47630.328-0.34841.4680.07140.0177-0.0964-0.3361-0.0487-0.03210.25980.0572-00.5872-0.05240.10320.23290.00030.3512-12.543932.270345.3371
80.62330.0655-0.2594-0.11210.08461.19520.06250.1388-0.0272-0.15070.0397-0.11450.5789-0.1893-0.13941.0042-0.2134-0.34420.43660.15160.664-36.21523.971639.6967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA5 - 900
2X-RAY DIFFRACTION2chain BB5 - 900
3X-RAY DIFFRACTION3chain CC5 - 900
4X-RAY DIFFRACTION4chain DD5 - 900
5X-RAY DIFFRACTION5chain EE5 - 900
6X-RAY DIFFRACTION6chain FF5 - 900
7X-RAY DIFFRACTION7chain GG5 - 900
8X-RAY DIFFRACTION8chain HH5 - 900

+
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