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- PDB-6qwq: Structure of gtPebB -

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Basic information

Entry
Database: PDB / ID: 6qwq
TitleStructure of gtPebB
ComponentsFerredoxin bilin reductase plastid
KeywordsOXIDOREDUCTASE / PHYCOBILIN SYNTHESIS / DIHYDROBILIVERDIN / PHYCOERYTHROBILIN / FERREDOXIN DEPENDENT BILIN REDUCTASE
Function / homologyoxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / phytochromobilin biosynthetic process / cobalt ion binding / Ferredoxin bilin reductase plastid
Function and homology information
Biological speciesGuillardia theta CCMP2712 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSommerkamp, J.A. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHO2600-3 Germany
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of the first eukaryotic bilin reductaseGtPEBB reveals a flipped binding mode of dihydrobiliverdin.
Authors: Sommerkamp, J.A. / Frankenberg-Dinkel, N. / Hofmann, E.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin bilin reductase plastid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4815
Polymers32,0961
Non-polymers3844
Water3,027168
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-42 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.600, 109.600, 47.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Ferredoxin bilin reductase plastid


Mass: 32096.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta CCMP2712 (eukaryote) / Gene: GUITHDRAFT_96430 / Plasmid: pGEX-4T1-TEV-gtPebB_cut70 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L1IWQ9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 34.5 % PEG3350, 0.21 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00601 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00601 Å / Relative weight: 1
ReflectionResolution: 1.9→47.458 Å / Num. obs: 25797 / % possible obs: 98.7 % / Redundancy: 19 % / Net I/σ(I): 15.31
Reflection shellResolution: 1.9→1.968 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSBUILT=20160617data reduction
XSCALEBUILT=20160617data scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.458 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2328 1295 5.02 %
Rwork0.211 --
obs0.2121 25795 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 20 168 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062291
X-RAY DIFFRACTIONf_angle_d0.7773109
X-RAY DIFFRACTIONf_dihedral_angle_d16.011354
X-RAY DIFFRACTIONf_chiral_restr0.045310
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.97620.31011380.33742612X-RAY DIFFRACTION97
1.9762-2.06620.32221430.30482691X-RAY DIFFRACTION97
2.0662-2.17510.31211410.29832696X-RAY DIFFRACTION98
2.1751-2.31140.31511440.27212692X-RAY DIFFRACTION99
2.3114-2.48990.28351460.24582727X-RAY DIFFRACTION99
2.4899-2.74040.27861430.24792722X-RAY DIFFRACTION99
2.7404-3.13690.28281440.22582753X-RAY DIFFRACTION99
3.1369-3.95180.2041450.18022766X-RAY DIFFRACTION100
3.9518-47.4730.17441510.16622841X-RAY DIFFRACTION100

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