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- PDB-3f0m: Crystal structure of radical D105N Synechocystis sp. PcyA -

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Basic information

Entry
Database: PDB / ID: 3f0m
TitleCrystal structure of radical D105N Synechocystis sp. PcyA
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA SANDWICH / RADICAL CHEMISTRY
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsKohler, A.C. / Gae, D.D.
CitationJournal: Biochemistry / Year: 2010
Title: Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants.
Authors: Kohler, A.C. / Gae, D.D. / Richley, M.A. / Stoll, S. / Gunn, A. / Lim, S. / Martin, S.S. / Doukov, T.I. / Britt, R.D. / Ames, J.B. / Lagarias, J.C. / Fisher, A.J.
History
DepositionOct 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Oct 20, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1729
Polymers28,1551
Non-polymers1,0178
Water5,116284
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.940, 95.158, 42.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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. (bacteria) / Strain: PCC 6803 / Gene: pcyA, slr0116 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 284 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / pH: 7
Details: 1.45M Ammonium sulfate, 0.15M NaCl, 0.1M Cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007
RadiationMonochromator: NI MIRROR + NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 3.2 % / Av σ(I) over netI: 4.6 / Number: 145803 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / D res high: 1.483 Å / D res low: 95.783 Å / Num. obs: 46021 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.7195.7885.110.0560.0563.4
4.746.7196.510.0620.0624
3.874.7496.410.070.074
3.353.8797.510.0770.0773.6
33.3599.510.0820.0823.9
2.74399.810.0880.0884
2.542.7499.910.0950.0954.1
2.372.5410010.0970.0974
2.242.3799.610.1040.1043.5
2.122.249810.1070.1073.2
2.022.129810.1220.1223.1
1.942.0297.910.130.133
1.861.9498.110.1590.1593
1.791.8698.810.1880.1883
1.731.7998.310.2360.2363
1.681.7398.610.2890.2892.9
1.631.6898.310.3310.3312.8
1.581.6397.410.370.372.7
1.541.5895.710.440.442.6
1.51.5490.510.5520.5522.5
ReflectionResolution: 1.5→42.56 Å / Num. obs: 46971 / % possible obs: 97.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.54 Å / % possible all: 90.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.612 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2266 5 %RANDOM
Rwork0.174 ---
obs0.176 45327 96.5 %-
all-46971 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--0.98 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 71 284 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222108
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.0042865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61324.53697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28515361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1411513
X-RAY DIFFRACTIONr_chiral_restr0.1210.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211577
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.51252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84722032
X-RAY DIFFRACTIONr_scbond_it2.8853856
X-RAY DIFFRACTIONr_scangle_it4.6614.5823
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 138 -
Rwork0.239 2896 -
obs--87.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4741-0.0625-0.04730.11640.03870.07880.01110.011-0.00250.0016-0.0047-0.0174-0.0118-0.0144-0.0064-0.01280.00190.0025-0.0051-0.0057-0.0156-9.4628-27.155618.3411
23.9952-1.11853.37070.3267-1.04943.6685-0.07130.06030.0459-0.0407-0.0117-0.1484-0.01620.06060.083-0.00660.00460.00980.0257-0.00690.0127-0.0454-27.258220.0253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 248
2X-RAY DIFFRACTION2A249

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