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- PDB-2x9o: STRUCTURE OF 15, 16- DIHYDROBILIVERDIN:FERREDOXIN OXIDOREDUCTASE ... -

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Basic information

Entry
Database: PDB / ID: 2x9o
TitleSTRUCTURE OF 15, 16- DIHYDROBILIVERDIN:FERREDOXIN OXIDOREDUCTASE (PebA)
Components15,16-DIHYDROBILIVERDIN-FERREDOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / PHYCOBILIN SYNTHESIS / CYANOBACTERIA / PHYCOERYTHROBILIN
Function / homology
Function and homology information


15,16-dihydrobiliverdin:ferredoxin oxidoreductase / 15,16-dihydrobiliverdin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding
Similarity search - Function
15,16-dihydrobiliverdin: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 / 15,16-dihydrobiliverdin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSYNECHOCOCCUS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsBusch, A.W.U. / Frankenberg-Dinkel, N. / Hofmann, E.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural and Mechanistic Insight Into the Ferredoxin-Mediated Two-Electron Reduction of Bilins.
Authors: Busch, A.W.U. / Reijerse, E.J. / Lubitz, W. / Frankenberg-Dinkel, N. / Hofmann, E.
History
DepositionMar 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references / Structure summary / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 15,16-DIHYDROBILIVERDIN-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7202
Polymers28,1371
Non-polymers5831
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 39.350, 71.270
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 15,16-DIHYDROBILIVERDIN-FERREDOXIN OXIDOREDUCTASE


Mass: 28137.084 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS SP. (bacteria) / Strain: WH8020 / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q02189, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST METHIONINE HAS BEEN REPLACED BY 9 RESIDUES FROM THE PLASMID CONSTRUCT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7 / Details: 100MM HEPES PH 7.0, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978946
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978946 Å / Relative weight: 1
ReflectionResolution: 1.55→40.18 Å / Num. obs: 33089 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.53
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.91 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.55→40.185 Å / SU ML: 0.17 / σ(F): 2 / Phase error: 21.61 / Stereochemistry target values: ML
Details: RESIDUES 128 AND 129 WERE NOT MODELLED DUE TO MISSING DENSITY
RfactorNum. reflection% reflection
Rfree0.2247 1655 5 %
Rwork0.1791 --
obs0.1813 33086 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.321 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.9508 Å20 Å21.6075 Å2
2--2.1651 Å2-0 Å2
3----5.1159 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 43 322 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072038
X-RAY DIFFRACTIONf_angle_d1.1642773
X-RAY DIFFRACTIONf_dihedral_angle_d16.079728
X-RAY DIFFRACTIONf_chiral_restr0.083272
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5499-1.59550.25541370.21932601X-RAY DIFFRACTION99
1.5955-1.6470.29351380.21412620X-RAY DIFFRACTION100
1.647-1.70590.24481360.20412592X-RAY DIFFRACTION100
1.7059-1.77420.23771370.1922587X-RAY DIFFRACTION100
1.7742-1.85490.2371370.18362608X-RAY DIFFRACTION100
1.8549-1.95270.24271370.1892610X-RAY DIFFRACTION100
1.9527-2.0750.22971390.182630X-RAY DIFFRACTION100
2.075-2.23520.2371370.17862618X-RAY DIFFRACTION100
2.2352-2.46010.21391370.17572599X-RAY DIFFRACTION100
2.4601-2.81610.24191380.18372616X-RAY DIFFRACTION99
2.8161-3.54760.21551390.16712647X-RAY DIFFRACTION99
3.5476-40.19860.19021430.15732703X-RAY DIFFRACTION100

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