[English] 日本語
Yorodumi
- PDB-4qcd: Neutron crystal structure of phycocyanobilin:ferredoxin oxidoredu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qcd
TitleNeutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / bilin reductase / biliverdin IXalpha
Function / homology
Function and homology information


phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding
Similarity search - Function
Phycocyanobilin:ferredoxin oxidoreductase / oxygen-dependent coproporphyrinogen oxidase - #20 / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / trideuteriooxidanium / Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsUnno, M. / Ishikawa-Suto, K. / Ishihara, M. / Hagiwara, Y. / Sugishima, M. / Wada, K. / Fukuyama, K.
CitationJournal: J. Am. Chem. Soc. / Year: 2015
Title: Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.
Authors: Unno, M. / Ishikawa-Suto, K. / Kusaka, K. / Tamada, T. / Hagiwara, Y. / Sugishima, M. / Wada, K. / Yamada, T. / Tomoyori, K. / Hosoya, T. / Tanaka, I. / Niimura, N. / Kuroki, R. / Inaka, K. ...Authors: Unno, M. / Ishikawa-Suto, K. / Kusaka, K. / Tamada, T. / Hagiwara, Y. / Sugishima, M. / Wada, K. / Yamada, T. / Tomoyori, K. / Hosoya, T. / Tanaka, I. / Niimura, N. / Kuroki, R. / Inaka, K. / Ishihara, M. / Fukuyama, K.
History
DepositionMay 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / diffrn_detector / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_detector.details / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 2.0Jun 9, 2021Group: Derived calculations / Non-polymer description / Category: chem_comp / struct_site
Item: _chem_comp.formula / _struct_site.pdbx_auth_asym_id ..._chem_comp.formula / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7613
Polymers28,1561
Non-polymers6052
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.107, 97.278, 43.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase /


Mass: 28156.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: pcyA, slr0116 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-D3O / trideuteriooxidanium / perdeuterated oxonium


Mass: 22.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: D3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND BLA WAS PROTONATED.

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: Ammonium Sulfate, NaCl, MES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12731
22731
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0313.0-5.6
SYNCHROTRONPhoton Factory AR-NE3A21
Detector
TypeIDDateDetailsDetector
1Apr 10, 2013WLS-fiber-based scintillator detector
ADSC QUANTUM 2702Nov 5, 2013CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Neutron time-of-flightLAUEMneutron1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
131
25.61
311
ReflectionResolution: 1.55→50 Å / Num. all: 44240 / Num. obs: 43975 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.55→1.58 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDPhase errorσ(F)
1.932-21.189NEUTRON DIFFRACTION0.22710.16710.17311839183791837910.0179.390.24117.55
1.551-36.904X-RAY DIFFRACTION0.16540.14310.1451382944184439198.7299.380.12217.261.34
Refinement stepCycle: LAST / Resolution: 1.932→21.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 44 185 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0114954
NEUTRON DIFFRACTIONf_angle_d1.3768534
NEUTRON DIFFRACTIONf_dihedral_angle_d23.761399
NEUTRON DIFFRACTIONf_chiral_restr0.06311
NEUTRON DIFFRACTIONf_plane_restr0.006939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9317-1.98390.3286750.2936672NEUTRON DIFFRACTION43
1.9839-2.04220.35181070.2573970NEUTRON DIFFRACTION62
2.0422-2.1080.28751160.23391040NEUTRON DIFFRACTION66
2.108-2.18330.27441280.2171153NEUTRON DIFFRACTION72
2.1833-2.27060.26261310.18451185NEUTRON DIFFRACTION75
2.2706-2.37390.23051440.1781281NEUTRON DIFFRACTION81
2.3739-2.49880.20641480.16671341NEUTRON DIFFRACTION85
2.4988-2.65510.22631560.16161405NEUTRON DIFFRACTION88
2.6551-2.85970.22281650.16511481NEUTRON DIFFRACTION93
2.8597-3.14660.21881660.15371491NEUTRON DIFFRACTION93
3.1466-3.60.21231690.13541534NEUTRON DIFFRACTION93
3.6-4.52830.16921690.11941521NEUTRON DIFFRACTION94
4.5283-21.19040.19161650.13521466NEUTRON DIFFRACTION85
1.5512-1.57080.23021240.19161464X-RAY DIFFRACTION99
1.5708-1.59150.21761250.17971479X-RAY DIFFRACTION99
1.5915-1.61330.19761240.17171460X-RAY DIFFRACTION98
1.6133-1.63640.17871250.15941479X-RAY DIFFRACTION100
1.6364-1.66080.23261260.15681497X-RAY DIFFRACTION98
1.6608-1.68670.17961240.16041468X-RAY DIFFRACTION100
1.6867-1.71440.17351250.16791470X-RAY DIFFRACTION100
1.7144-1.74390.171260.1641490X-RAY DIFFRACTION99
1.7439-1.77570.19221260.15161490X-RAY DIFFRACTION100
1.7757-1.80980.19831270.15931486X-RAY DIFFRACTION99
1.8098-1.84680.19311230.16031466X-RAY DIFFRACTION100
1.8468-1.88690.21131270.15911503X-RAY DIFFRACTION99
1.8869-1.93080.19841270.15411490X-RAY DIFFRACTION100
1.9308-1.97910.19251400.15471488X-RAY DIFFRACTION100
1.9791-2.03260.16951510.14621488X-RAY DIFFRACTION100
2.0326-2.09240.17531490.14491457X-RAY DIFFRACTION100
2.0924-2.15990.16421520.1471481X-RAY DIFFRACTION100
2.1599-2.23710.17291530.14191460X-RAY DIFFRACTION100
2.2371-2.32670.16261570.14341486X-RAY DIFFRACTION100
2.3267-2.43250.15691570.14471476X-RAY DIFFRACTION100
2.4325-2.56080.14951610.14251494X-RAY DIFFRACTION100
2.5608-2.72110.15941590.15281480X-RAY DIFFRACTION100
2.7211-2.93120.19291620.15821473X-RAY DIFFRACTION100
2.9312-3.2260.16771650.15251513X-RAY DIFFRACTION100
3.226-3.69240.17021660.12911513X-RAY DIFFRACTION100
3.6924-4.65060.13031650.10781515X-RAY DIFFRACTION99
4.6506-36.91460.14641630.1381524X-RAY DIFFRACTION94

+
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