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- PDB-3i95: Crystal structure of E76Q mutant PcyA-biliverdin complex -

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Basic information

Entry
Database: PDB / ID: 3i95
TitleCrystal structure of E76Q mutant PcyA-biliverdin complex
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich / mutant enzyme-substrate complex
Function / homology
Function and homology information


phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin: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 / DIFFERENCE FOURIER / Resolution: 1.4 Å
AuthorsHagiwara, Y. / Sugishima, M. / Fukuyama, K.
CitationJournal: To be Published
Title: Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).
Authors: Hagiwara, Y. / Sugishima, M. / Khawn, H. / Kinoshita, H. / Inomata, K. / Shang, L. / Lagarias, J.C. / Takahashi, Y. / Fukuyama, K.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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)28,7382
Polymers28,1551
Non-polymers5831
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.681, 95.701, 42.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase /


Mass: 28155.170 Da / Num. of mol.: 1 / Mutation: E76Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: pcyA, slr0116 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q55891
#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 / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M ammonium sulfate, 2% PEG 400, 0.1M HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 26, 2009
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→17.98 Å / Num. obs: 57594 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.295 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2D1E

2d1e


Resolution: 1.4→17.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.858 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2929 5.1 %RANDOM
Rwork0.175 ---
obs0.176 57590 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.44 Å2 / Biso mean: 16.171 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 44 334 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222167
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9952943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.957115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46715405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3421515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021672
X-RAY DIFFRACTIONr_nbd_refined0.2020.21105
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.245
X-RAY DIFFRACTIONr_mcbond_it0.6771.51288
X-RAY DIFFRACTIONr_mcangle_it1.1222045
X-RAY DIFFRACTIONr_scbond_it1.6631004
X-RAY DIFFRACTIONr_scangle_it2.4864.5898
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 214 -
Rwork0.231 3913 -
all-4127 -
obs--97.82 %

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