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- PDB-7ykb: Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin ... -

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Basic information

Entry
Database: PDB / ID: 7ykb
TitleNeutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / phycocyanobilin / ferredoxin oxi-doreductase / neutron / hydrogen / proton / mutant / reaction / absorption spectrum
Function / homologyphycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / Phycocyanobilin:ferredoxin oxidoreductase / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / phytochromobilin biosynthetic process / cobalt ion binding / Chem-BLR / Phycocyanobilin:ferredoxin oxidoreductase
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsUnno, M. / Nanasawa, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07261 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states.
Authors: Joutsuka, T. / Nanasawa, R. / Igarashi, K. / Horie, K. / Sugishima, M. / Hagiwara, Y. / Wada, K. / Fukuyama, K. / Yano, N. / Mori, S. / Ostermann, A. / Kusaka, K. / Unno, M.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,7633
Polymers28,1551
Non-polymers6082
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.174, 97.523, 43.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase


Mass: 28155.172 Da / Num. of mol.: 1 / Mutation: D105N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: Kazusa / Gene: pcyA / Production host: Escherichia coli (E. coli)
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BLR / 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / Bilirubin IX alpha


Mass: 584.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NaCl, ammonium sulfate, MES

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
13001N
23001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.63-6.06
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 2M1PIXELJun 6, 2021
iBIX2DIFFRACTOMETERMar 20, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.631
36.061
Reflection

Biso Wilson estimate: 15.07 Å2 / Entry-ID: 7YKB

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Diffraction-IDNet I/σ(I)
1.38-43.286240299.64.90.997112.2
2.1-21.161815899.36.93770.982829.18
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.38-1.430990.7521
2.1-2.1717950.47892

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMACphasing
Refinement

SU ML: 0.1322 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.9555 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3F0M

3f0m

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.38-34.58X-RAY DIFFRACTION17.930.17160.15010.1505112761232623591.8199.3411.35
2.1-21.12NEUTRON DIFFRACTION0.18060.16571815898.68472
Refinement stepCycle: LAST / Resolution: 1.38→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 44 219 2188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162228
X-RAY DIFFRACTIONf_angle_d1.46083075
X-RAY DIFFRACTIONf_chiral_restr0.0921325
X-RAY DIFFRACTIONf_plane_restr0.0117499
X-RAY DIFFRACTIONf_dihedral_angle_d19.4914909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.440.26421400.2397621X-RAY DIFFRACTION99.87
1.44-1.520.24721410.217579X-RAY DIFFRACTION99.99
1.52-1.610.19671400.1867609X-RAY DIFFRACTION99.95
1.61-1.740.20681410.17187632X-RAY DIFFRACTION99.77
1.74-1.910.19551400.16537621X-RAY DIFFRACTION99.74
1.91-2.190.16781430.14357664X-RAY DIFFRACTION99.44
2.19-2.760.16891410.14017688X-RAY DIFFRACTION99.1
2.76-34.580.14451410.13117818X-RAY DIFFRACTION96.99

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