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- PDB-5b4j: Crystal structure of I86D mutant of phycocyanobilin:ferredoxin ox... -

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Basic information

Entry
Database: PDB / ID: 5b4j
TitleCrystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 3)
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / Photosynthesis pigment / heme metabolism
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 / Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsHagiwara, Y. / Wada, K. / Irikawa, T. / Unno, M. / Fukuyama, K. / Sugishima, M.
Funding support Japan, 7items
OrganizationGrant numberCountry
JSPS20370037 Japan
JSPS22770096 Japan
JSPS23370052 Japan
JSPS24570122 Japan
JSPS24870030 Japan
JSPS25840026 Japan
Program to Dissiminate Tenura Tracking Japan
CitationJournal: FEBS Lett. / Year: 2016
Title: Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin
Authors: Hagiwara, Y. / Wada, K. / Irikawa, T. / Sato, H. / Unno, M. / Yamamoto, K. / Fukuyama, K. / Sugishima, M.
History
DepositionApr 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7412
Polymers28,1581
Non-polymers5831
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-17 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.823, 95.861, 42.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

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Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase


Mass: 28158.086 Da / Num. of mol.: 1 / Mutation: I86D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Gene: pcyA / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.55 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, sodium chloride, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→56.97 Å / Num. obs: 134801 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rsym value: 0.065 / Net I/σ(I): 9.7
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.378 / % possible all: 99.3

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Processing

Software
NameClassification
SHELXL-97refinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4QCD

4qcd


Resolution: 1.05→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1677 -5 %RANDOM
Rwork0.1388 ---
all-127522 --
obs-127522 100 %-
Refine analyzeNum. disordered residues: 36 / Occupancy sum non hydrogen: 2314.9
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 43 368 2453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0146
X-RAY DIFFRACTIONs_angle_d0.0316
X-RAY DIFFRACTIONs_zero_chiral_vol0.0917
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0878
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0367
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0498
X-RAY DIFFRACTIONs_approx_iso_adps0.1622

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