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- PDB-6kme: Crystal structure of phytochromobilin synthase from tomato in com... -

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Basic information

Entry
Database: PDB / ID: 6kme
TitleCrystal structure of phytochromobilin synthase from tomato in complex with biliverdin
ComponentsPhytochromobilin synthase
KeywordsOXIDOREDUCTASE / Substrate complex
Function / homologyphytochromobilin:ferredoxin oxidoreductase / phytochromobilin:ferredoxin oxidoreductase activity / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / phytochromobilin biosynthetic process / cobalt ion binding / BILIVERDINE IX ALPHA / Phytochromobilin synthase
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSugishima, M. / Wada, K. / Fukuyama, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science19K06515 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of phytochromobilin synthase in complex with biliverdin IX alpha , a key enzyme in the biosynthesis of phytochrome.
Authors: Sugishima, M. / Wada, K. / Fukuyama, K. / Yamamoto, K.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochromobilin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2264
Polymers36,5831
Non-polymers6423
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-17 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.130, 64.130, 158.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Phytochromobilin synthase


Mass: 36583.461 Da / Num. of mol.: 1 / Mutation: T116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: AUREA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q588D6, phytochromobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 8000, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.851 Å / Num. obs: 25049 / % possible obs: 100 % / Redundancy: 95.059 % / Biso Wilson estimate: 31.466 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.534 / Rpim(I) all: 0.055 / Rrim(I) all: 0.537 / Χ2: 1.064 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-2.0691.2574.2223.8137190.9590.4474.246100
2.06-2.293.7662.75.8937130.9632.714100
2.2-2.3793.9991.6988.6334220.981.708100
2.37-2.693.3791.02412.7233360.9881.03100
2.6-2.998.0720.65118.0629400.9940.654100
2.9-3.35100.7110.42525.9126850.9940.427100
3.35-4.198.5940.29337.0522860.9960.294100
4.1-5.7793.6370.2341.9118240.9970.232100
5.77-49.85193.8540.18443.6511240.9980.18599.6

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Processing

Software
NameVersionClassification
PHENIXv1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMD

6kmd


Resolution: 1.95→49.851 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1245 4.99 %RANDOM
Rwork0.1623 23716 --
obs0.1646 24961 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.82 Å2 / Biso mean: 32.981 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 1.95→49.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 45 246 2561
Biso mean--27.78 40.09 -
Num. residues----284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.95-2.02810.27071340.19662568
2.0281-2.12040.2521340.18512557
2.1204-2.23220.22751330.17382596
2.2322-2.3720.20981320.16592607
2.372-2.55520.21361270.16342607
2.5552-2.81230.22491450.18232618
2.8123-3.21920.25211600.17342625
3.2192-4.05550.18631370.14682676
4.0555-49.8510.1661430.14862862
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)
12.09921.8691.57073.35853.20384.70480.3057-0.0697-0.35930.3136-0.0586-0.170.54650.1445-0.23310.2937-0.0117-0.090.17570.04220.218164.439719.584177.8223
23.6014-0.2184-1.73143.06241.06015.18160.23670.010.15270.1301-0.20370.0599-0.27990.0355-0.01510.1738-0.0614-0.03090.20480.00380.150364.526735.920972.2929
31.59140.40940.56271.19850.26973.23960.1033-0.14020.10180.1209-0.08850.0644-0.19660.1215-0.03310.1974-0.04940.00460.1149-0.02280.197362.017235.811171.9493
45.4537-1.305-1.42667.66393.41258.64840.03230.1626-0.2192-0.0883-0.02950.1190.1816-0.4315-0.00880.1407-0.0163-0.05680.13720.00640.190955.05118.00763.6891
52.80460.60470.24822.2497-0.55672.95510.17310.02940.1646-0.0314-0.07240.2697-0.1794-0.1479-0.05670.19610.02970.02870.0912-0.05290.185551.725236.413463.5526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 114 )A56 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 184 )A115 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 262 )A185 - 262
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 284 )A263 - 284
5X-RAY DIFFRACTION5chain 'A' and (resid 285 through 336 )A285 - 336

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