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- PDB-3f0l: Crystal structure of oxidized D105N Synechocystis sp. PcyA -

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Basic information

Entry
Database: PDB / ID: 3f0l
TitleCrystal structure of oxidized 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: 1.3 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)29,42113
Polymers28,1551
Non-polymers1,26512
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.845, 95.554, 42.690
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.: 11 / 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.: 298 / 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 / pH: 7
Details: 1.45M Ammonium sulfate, 0.15M NaCl, 0.1M Aacodylate, 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: 4.1 % / Av σ(I) over netI: 8.9 / Number: 286749 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / D res high: 1.3 Å / D res low: 23.682 Å / Num. obs: 69979 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.8123.6889.810.040.046.8
4.115.8196.210.0380.0387
3.364.1197.510.0360.0367.2
2.913.3697.910.040.047.4
2.62.9198.610.0470.0477.4
2.372.699.110.0540.0547.3
2.22.3799.510.0620.0626.6
2.062.299.310.0690.0696.1
1.942.0699.310.0760.0765.7
1.841.9499.110.0890.0895.3
1.751.8494.510.10.14.6
1.681.7598.210.1130.1134.1
1.611.6897.810.1360.1363.9
1.551.6197.910.1670.1673.8
1.51.559810.2070.2073.6
1.451.597.610.1290.1291.8
1.411.4597.410.1430.1431.7
1.371.4197.510.1670.1671.6
1.331.3796.710.2040.2041.6
1.31.3395.410.2070.2071.6
ReflectionResolution: 1.3→39.62 Å / Num. obs: 72066 / % possible obs: 97.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.33 Å / % possible all: 95.4

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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: 1.3→39.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.488 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3463 5 %RANDOM
Rwork0.169 ---
obs0.17 69947 97.1 %-
all-72066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--1.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 87 298 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7212.0082972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80524.854103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.441513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211633
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_it0.8941.51280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57322087
X-RAY DIFFRACTIONr_scbond_it2.4963904
X-RAY DIFFRACTIONr_scangle_it3.8594.5865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 227 -
Rwork0.26 4783 -
obs--94.6 %
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)
10.6859-0.0212-0.01360.17920.06450.15030.00920.0099-0.0150.0036-0.0086-0.0215-0.0113-0.0263-0.0006-0.01440.00350.0015-0.0209-0.0013-0.0047-9.482-27.32218.394
20.9202-0.2426-0.32591.4809-0.35614.359-0.02550.0759-0.0988-0.02260.0511-0.0583-0.01350.0067-0.0257-0.01130.00420.0016-0.01930.00040.0431-0.004-27.26420.281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 248
2X-RAY DIFFRACTION2A249

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