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- PDB-6g20: Crystal structure of a fluorescence optimized bathy phytochrome P... -

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Basic information

Entry
Database: PDB / ID: 6g20
TitleCrystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its functional Meta-F intermediate state.
ComponentsBacteriophytochrome protein
KeywordsFLUORESCENT PROTEIN / SIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / META-F STATE / LIGHT ADAPTATION / BATHY PHYTOCHROME / PHOTOSENSORY CORE MODULE / OPTOGENETIC / FLOURESCENCE
Function / homology
Function and homology information


protein histidine kinase activity / detection of visible light / histidine kinase / photoreceptor activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region ...Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / 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. / GAF domain / PAS domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / GAF domain / CheY-like superfamily / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EL5 / Chem-ETE / DI(HYDROXYETHYL)ETHER / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsSchmidt, A. / Sauthof, L. / Szczepek, M. / Scheerer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
SFB1078 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural snapshot of a bacterial phytochrome in its functional intermediate state.
Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / ...Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / Krauss, N. / Lamparter, T. / Hildebrandt, P. / Scheerer, P.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome protein
B: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71436
Polymers113,3572
Non-polymers4,35734
Water5,603311
1
A: Bacteriophytochrome protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)353,100108
Polymers340,0726
Non-polymers13,028102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area48710 Å2
ΔGint-1036 kcal/mol
Surface area114330 Å2
MethodPISA
2
B: Bacteriophytochrome protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)353,184108
Polymers340,0726
Non-polymers13,113102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area45600 Å2
ΔGint-922 kcal/mol
Surface area120800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.114, 183.114, 179.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

21A-602-

SO4

31A-610-

SO4

41A-610-

SO4

51B-602-

SO4

61B-602-

SO4

71B-609-

SO4

81B-609-

SO4

91B-611-

SO4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacteriophytochrome protein


Mass: 56678.590 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: SY94_2021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81

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Non-polymers , 8 types, 345 molecules

#2: Chemical ChemComp-EL5 / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid / biliverdin, bound form at Pfr state / Biliverdin


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#8: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: (NH4)2SO4, VAPOR DIFFUSION, TEMPERATURE 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.16→47.79 Å / Num. obs: 95000 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 18.3
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 13679 / CC1/2: 0.672 / Rpim(I) all: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1Z

6g1z


Resolution: 2.16→158.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.027 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23225 4842 5.1 %RANDOM
Rwork0.20905 ---
obs0.2102 90118 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.886 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21.01 Å20 Å2
2--2.01 Å2-0 Å2
3----6.53 Å2
Refinement stepCycle: 1 / Resolution: 2.16→158.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 262 311 8085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028115
X-RAY DIFFRACTIONr_bond_other_d0.0150.0217726
X-RAY DIFFRACTIONr_angle_refined_deg1.4682.01411047
X-RAY DIFFRACTIONr_angle_other_deg0.8353.01617721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48951017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45722.486358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.358151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9681579
X-RAY DIFFRACTIONr_chiral_restr0.0710.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219057
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021898
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_it1.4232.3963924
X-RAY DIFFRACTIONr_mcbond_other1.422.3953923
X-RAY DIFFRACTIONr_mcangle_it2.4273.5724906
X-RAY DIFFRACTIONr_mcangle_other2.4263.5744907
X-RAY DIFFRACTIONr_scbond_it1.8622.8164191
X-RAY DIFFRACTIONr_scbond_other1.8622.8174192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0234.1096112
X-RAY DIFFRACTIONr_long_range_B_refined6.96119.8158940
X-RAY DIFFRACTIONr_long_range_B_other6.96119.8218941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 364 -
Rwork0.299 6572 -
obs--100 %
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)
11.2992-0.521-0.36531.33760.80071.36130.11440.0986-0.0893-0.0408-0.0431-0.03110.04520.1318-0.07130.01940.0218-0.05510.038-0.00310.65617.27-39.036-28.044
20.4778-0.3271-0.49690.28660.3991.2387-0.0326-0.0023-0.06860.0058-0.00370.0999-0.0128-0.07060.03630.00810.0040.01350.008-0.01570.825456.561-49.697-32.852
30.1881-0.0338-0.19391.22490.45390.7872-0.0181-0.0491-0.0050.07980.09290.03990.06440.0082-0.07480.0336-0.0054-0.03750.04480.02070.7122-2.713-28.67912.074
400000000000000-00.6487000.648700.6487000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 306
2X-RAY DIFFRACTION2B5 - 306
3X-RAY DIFFRACTION3A307 - 506
4X-RAY DIFFRACTION4B307 - 507

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