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- PDB-2d1e: Crystal structure of PcyA-biliverdin complex -

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Basic information

Entry
Database: PDB / ID: 2d1e
TitleCrystal structure of PcyA-biliverdin complex
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich / enzyme-substrate 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
BILIVERDINE IX ALPHA / Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.51 Å
AuthorsHagiwara, Y. / Sugishima, M. / Takahashi, Y. / Fukuyama, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin
Authors: Hagiwara, Y. / Sugishima, M. / Takahashi, Y. / Fukuyama, K.
History
DepositionAug 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7623
Polymers28,1561
Non-polymers6062
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.826, 94.997, 42.675
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-1186-

HOH

DetailsThe biological assembly is a monomer in the asymmetric unit.

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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. (bacteria) / Strain: PCC 6803 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


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


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, sodium cacodylate, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2005
RadiationMonochromator: Si (111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
7.31202130.0891.022299.8
72234080.0811.0011.999.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315097.810.0691.6236.6
3.424.3110010.0641.1537.3
2.993.4210010.0711.0227.4
2.712.9910010.0910.987.4
2.522.7110010.1080.9097.5
2.372.5210010.1260.8957.5
2.252.3710010.1560.9227.4
2.152.2510010.1781.0747.3
2.072.1510010.1950.8367.3
22.0710010.2350.8317.2
4.095098.220.0581.3096.7
3.254.0999.720.0580.9717.1
2.843.2599.820.0730.9917.2
2.582.8499.920.0931.0167.3
2.392.5899.920.1121.0397.2
2.252.3999.920.1230.9777.1
2.142.2599.920.1420.9527
2.052.1499.820.1710.9326.9
1.972.0599.620.2140.8976.8
1.91.9799.420.2850.9166.8
ReflectionResolution: 1.51→50 Å / Num. all: 45715 / Num. obs: 45715 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.078 / Χ2: 1.052
Reflection shellResolution: 1.51→1.56 Å / % possible obs: 98 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.335 / Num. measured obs: 4400 / Χ2: 0.784 / % possible all: 98

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Phasing

PhasingMethod: MIRAS
Phasing dmDelta phi final: 11.84 / Delta phi initial: 38.24 / FOM : 0.836 / Mask type: RMS / Method: FLIP / Reflection: 89555
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.3-500.012.1340.9062028
4.2-5.35.4170.9512049
3.67-4.28.6280.952049
3.34-3.679.4760.9222017
3.1-3.349.7090.922035
2.91-3.110.9730.9242047
2.77-2.9112.7580.8912042
2.65-2.7710.2390.8982025
2.55-2.6512.5310.8822038
2.46-2.5511.6680.8832065
2.38-2.4612.2560.8761984
2.31-2.3811.9580.8632066
2.25-2.3113.3940.8661978
2.2-2.2514.5870.8672103
2.15-2.214.4390.8532013
2.1-2.1515.1550.8322051
2.06-2.116.1720.8252003
2.02-2.0614.2730.8312037
1.98-2.0215.0190.832062
1.95-1.9814.1130.8252002
1.92-1.9514.5240.8172053
1.89-1.9212.5980.8342040
1.86-1.8911.810.822000
1.84-1.8610.2660.8182053
1.81-1.8410.7590.8172052
1.79-1.8110.9140.8172031
1.77-1.7911.5320.8062000
1.74-1.7711.6830.7672092
1.72-1.7411.760.7951967
1.7-1.7211.080.8012071
1.69-1.710.5020.7982054
1.67-1.6911.4110.7972040
1.65-1.6711.9320.7852009
1.63-1.6513.090.7882062
1.62-1.6312.6750.7752008
1.6-1.6212.1440.7682041
1.59-1.613.3580.7222036
1.58-1.5912.5940.7712022
1.56-1.5812.1530.7622033
1.55-1.5611.7780.792081
1.54-1.5512.0860.7741994
1.52-1.5412.3090.7812044
1.51-1.5211.2170.8892038
1.5-1.5111.7950.8742040

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MIRAS / Resolution: 1.51→47.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.113 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2304 5 %RANDOM
Rwork0.157 ---
all0.158 45672 --
obs0.158 45672 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.51→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 44 363 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222118
X-RAY DIFFRACTIONr_bond_other_d0.0030.021932
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9982876
X-RAY DIFFRACTIONr_angle_other_deg1.03834532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16324.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52615386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6181514
X-RAY DIFFRACTIONr_chiral_restr0.10.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022302
X-RAY DIFFRACTIONr_gen_planes_other0.020.02411
X-RAY DIFFRACTIONr_nbd_refined0.2290.2477
X-RAY DIFFRACTIONr_nbd_other0.1930.22087
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21013
X-RAY DIFFRACTIONr_nbtor_other0.0890.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2256
X-RAY DIFFRACTIONr_metal_ion_refined0.2470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.232
X-RAY DIFFRACTIONr_mcbond_it1.031.51232
X-RAY DIFFRACTIONr_mcbond_other0.291.5485
X-RAY DIFFRACTIONr_mcangle_it1.82922014
X-RAY DIFFRACTIONr_scbond_it2.6523919
X-RAY DIFFRACTIONr_scangle_it4.2744.5862
LS refinement shellResolution: 1.512→1.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 161 -
Rwork0.223 3065 -
all-3226 -
obs--96.7 %

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