[English] 日本語
Yorodumi
- PDB-3i94: Crystal structure of PcyA-biliverdin XIII alpha complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i94
TitleCrystal structure of PcyA-biliverdin XIII alpha complex
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich / enzyme-substrate analog complex
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
Chem-BL3 / Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.04 Å
AuthorsHagiwara, Y. / Sugishima, M. / Fukuyama, K.
CitationJournal: to be published
Title: Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).
Authors: Hagiwara, Y. / Sugishima, M. / Khawn, H. / Kinoshita, H. / Inomata, K. / Shang, L. / Lagarias, J.C. / Takahashi, Y. / Fukuyama, K.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8353
Polymers28,1561
Non-polymers6792
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.785, 94.797, 42.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-9140-

HOH

21A-9182-

HOH

-
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. PCC 6803 (bacteria) / Gene: pcyA, slr0116 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BL3 / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy l]-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / BILIVERDIN XIII ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate (pH 7.0), vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7085 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 1.04→28.94 Å / Num. obs: 134142 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.279 / % possible all: 98.9

-
Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHELXLrefinement
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2D1E

2d1e


Resolution: 1.04→28.94 Å / Occupancy max: 1 / Occupancy min: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflectionSelection details
Rfree0.148 -RANDOM
Rwork0.125 --
obs0.125 134142 -
all-134142 -
Displacement parametersBiso max: 87.9 Å2 / Biso mean: 19.363 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: LAST / Resolution: 1.04→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 48 376 3895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d2.75
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.04→1.08 Å / % reflection obs: 98.9 %

+
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