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- PDB-4our: Crystal structure of Arabidopsis thaliana phytochrome B photosens... -

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Basic information

Entry
Database: PDB / ID: 4our
TitleCrystal structure of Arabidopsis thaliana phytochrome B photosensory module
Components(Phytochrome B) x 2
KeywordsGENE REGULATION / N-terminal extension / PAS domain / GAF domain / PHY domain / hairpin / photosensor / signal transduction / Phytochrome interacting factor / phytochromobilin / cytosol/nucleus / TRANSCRIPTION
Function / homology
Function and homology information


abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system ...abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / red or far-red light photoreceptor activity / stomatal complex development / regulation of photoperiodism, flowering / gravitropism / regulation of seed germination / jasmonic acid mediated signaling pathway / response to far red light / phototropism / photomorphogenesis / detection of visible light / entrainment of circadian clock / response to temperature stimulus / phosphorelay sensor kinase activity / photosynthesis / response to cold / promoter-specific chromatin binding / chromatin organization / sequence-specific DNA binding / nuclear body / nuclear speck / negative regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region ...Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-O6E / TRIETHYLENE GLYCOL / Phytochrome B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSethe Burgie, E. / Bussell, A.N. / Walker, J.M. / Dubiel, K. / Vierstra, R.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome.
Authors: Burgie, E.S. / Bussell, A.N. / Walker, J.M. / Dubiel, K. / Vierstra, R.D.
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 2.0Oct 13, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Phytochrome B
B: Phytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83418
Polymers120,2692
Non-polymers2,56416
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-142 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.502, 127.502, 300.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Phytochrome B


Mass: 60346.887 Da / Num. of mol.: 1 / Fragment: photosensory module, UNP residues 90-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g18790, HY3, MSF3.17, PHYB / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P14713
#2: Protein Phytochrome B


Mass: 59922.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYB, HY3, At2g18790, MSF3.17 / Production host: Escherichia coli (E. coli) / References: UniProt: P14713

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Non-polymers , 5 types, 21 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-O6E / 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHESE RESIDUES ARE PART OF THE MAIN PHYTOCHROME CHAIN. THEY WERE NAMED UNK, BECAUSE THE REGISTRY OF ...THESE RESIDUES ARE PART OF THE MAIN PHYTOCHROME CHAIN. THEY WERE NAMED UNK, BECAUSE THE REGISTRY OF THE SEQUENCE CANNOT BE CLEARLY DEFINED FOR THOSE RESIDUES.

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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: 5.08 Å3/Da / Density % sol: 75.8 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: magnesium sulfate, polyethylene glycol 3340, glycerol, bistris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97896 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2012 / Details: beryllium lens
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97896 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 35084 / Num. obs: 35082 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.4-3.591100
3.59-3.831100
3.83-4.151100
4.15-4.611100
4.61-5.41100
5.4-501100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEA

2vea


Resolution: 3.4→49.565 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1750 5.01 %random
Rwork0.2425 ---
all0.2439 36731 --
obs0.2439 34960 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→49.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6910 0 163 5 7078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027214
X-RAY DIFFRACTIONf_angle_d0.579759
X-RAY DIFFRACTIONf_dihedral_angle_d12.6212649
X-RAY DIFFRACTIONf_chiral_restr0.0211092
X-RAY DIFFRACTIONf_plane_restr0.0021228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.50.36611410.33562673X-RAY DIFFRACTION100
3.5-3.61290.34941440.32472737X-RAY DIFFRACTION100
3.6129-3.7420.36221420.29032706X-RAY DIFFRACTION100
3.742-3.89180.28631440.2812722X-RAY DIFFRACTION100
3.8918-4.06880.29221440.26062726X-RAY DIFFRACTION100
4.0688-4.28320.2461430.23262735X-RAY DIFFRACTION100
4.2832-4.55140.24451450.21612764X-RAY DIFFRACTION100
4.5514-4.90250.21971450.19522750X-RAY DIFFRACTION100
4.9025-5.39540.23941460.21922766X-RAY DIFFRACTION100
5.3954-6.17480.30571480.24972804X-RAY DIFFRACTION100
6.1748-7.77480.27111490.24042832X-RAY DIFFRACTION100
7.7748-49.57030.24191590.22082995X-RAY DIFFRACTION100
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)
16.2893-0.63012.44225.39240.06845.5669-0.0659-0.6908-0.01340.42010.1502-0.4916-0.02750.4201-0.11310.76340.02870.05320.6951-0.06580.591938.036645.0951321.7675
22.389-0.59220.84332.90820.87883.6495-0.0763-0.19650.3151-0.1563-0.06520.0682-0.6277-0.39580.09410.85340.1422-0.00080.7388-0.05620.60921.463.0843313.878
35.2753-3.1977-2.06461.78661.06861.51961.13311.09470.3305-0.323-0.97380.7502-0.2118-1.9718-0.24731.73060.3116-0.13122.064-0.03471.3016-12.770873.1546300.2426
47.8299-0.1464-1.2395.2689-0.3198.06510.24650.0484-0.7654-0.4075-0.46480.527-0.183-0.48190.14120.91740.1692-0.1160.7895-0.1450.616513.744554.2206296.2786
50.38710.63470.05035.3201-0.61260.1151-0.321-0.9376-0.49090.0409-0.52552.4695-1.1662-3.07830.85171.60340.5806-0.22514.1016-0.56112.1942-14.879969.113310.1654
68.3009-4.0521-4.97232.50722.47553.04390.2440.74510.36930.04760.18050.2126-0.14160.0225-0.37420.9661-0.04740.01280.7902-0.12050.571725.607184.5213352.9667
75.26151.265-0.3856.40110.54465.14590.02380.10230.14580.20930.084-0.64010.19410.5267-0.16640.73190.12040.03590.9901-0.18210.788545.52375.5813343.2387
83.47250.1705-0.91681.26340.64822.56860.21650.28040.0865-0.0637-0.25910.23110.0435-0.59450.01550.86190.0281-0.01510.8641-0.11850.653114.45970.7792345.0718
92.2282-1.70570.68711.1888-0.27474.3919-0.25290.1697-0.1534-0.53380.24760.435-1.2093-1.6545-0.0151.30910.07350.01011.5496-0.21181.049-10.702280.8254354.3475
104.09860.76891.07772.3995-0.25975.093-0.20640.03120.6458-0.1967-0.02060.7296-0.7063-1.73160.23881.24940.19120.05871.5434-0.21180.81430.059577.8793354.7957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 101 through 223 )
2X-RAY DIFFRACTION2chain 'A' and (resid 224 through 448 )
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 569 )
4X-RAY DIFFRACTION4chain 'A' and (resid 570 through 590 )
5X-RAY DIFFRACTION5chain 'A' and (resid 591 through 617 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 117 )
7X-RAY DIFFRACTION7chain 'B' and (resid 118 through 223 )
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 508 )
9X-RAY DIFFRACTION9chain 'B' and (resid 509 through 574 )
10X-RAY DIFFRACTION10chain 'B' and (resid 575 through 610 )

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