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- PDB-3ajg: Crystal structure of PcyA V225D-biliverdin IX alpha complex -

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Basic information

Entry
Database: PDB / ID: 3ajg
TitleCrystal structure of PcyA V225D-biliverdin IX alpha complex
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / alpha/beta/alpha sandwich
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWada, K. / Hagiwara, Y. / Fukuyama, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: One residue substitution in PcyA leads to unexpected changes in tetrapyrrole substrate binding.
Authors: Wada, K. / Hagiwara, Y. / Yutani, Y. / Fukuyama, K.
History
DepositionJun 5, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phycocyanobilin:ferredoxin oxidoreductase
B: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5104
Polymers56,3442
Non-polymers1,1652
Water3,639202
1
A: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7552
Polymers28,1721
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7552
Polymers28,1721
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.046, 74.875, 84.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase


Mass: 28172.113 Da / Num. of mol.: 2 / Mutation: V225D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: pcyA, slr0116 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / 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.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.8-1.0M NaH2PO4, 1.0-1.2M K2HPO4, 100mM sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2009
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 36692 / Num. obs: 36692 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.37 / Num. unique all: 3623 / % possible all: 99.6

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D1E

2d1e


Resolution: 1.9→32.88 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.257 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29483 1842 5 %RANDOM
Rwork0.23081 ---
all0.2316 34843 --
obs0.23403 34843 98.31 %-
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 mean: 36.837 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 86 202 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223997
X-RAY DIFFRACTIONr_bond_other_d0.0010.025
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.9945442
X-RAY DIFFRACTIONr_angle_other_deg0.67239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8295476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.70724.639194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49215653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6721525
X-RAY DIFFRACTIONr_chiral_restr0.1370.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025
X-RAY DIFFRACTIONr_nbd_refined0.240.21869
X-RAY DIFFRACTIONr_nbd_other0.2580.22
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22678
X-RAY DIFFRACTIONr_nbtor_other0.2890.26
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.27
X-RAY DIFFRACTIONr_mcbond_it1.3461.52493
X-RAY DIFFRACTIONr_mcbond_other0.1941.53
X-RAY DIFFRACTIONr_mcangle_it2.04523881
X-RAY DIFFRACTIONr_scbond_it2.86831749
X-RAY DIFFRACTIONr_scangle_it4.234.51561
LS refinement shellResolution: 1.905→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 107 -
Rwork0.215 2486 -
obs--96.22 %

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