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- PDB-8bor: Photosensory module from DrBphP without PHY tongue -

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Basic information

Entry
Database: PDB / ID: 8bor
TitlePhotosensory module from DrBphP without PHY tongue
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / KINASE / PHOTOSENSOR / PHYTOCHROME
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / 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-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKurttila, M. / Takala, H. / Ihalainen, J.A.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland330678 Finland
Academy of Finland332742 Finland
CitationJournal: Structure / Year: 2023
Title: The interconnecting hairpin extension "arm": An essential allosteric element of phytochrome activity.
Authors: Kurttila, M. / Rumfeldt, J. / Takala, H. / Ihalainen, J.A.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,7418
Polymers213,3984
Non-polymers2,3434
Water7,674426
1
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8704
Polymers106,6992
Non-polymers1,1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-45 kcal/mol
Surface area37480 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8704
Polymers106,6992
Non-polymers1,1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-47 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.630, 64.590, 131.040
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 53349.484 Da / Num. of mol.: 4 / Mutation: Residues 446-477 replaced with 'GGGS'
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 NCIMB 9279 / R1 / VKM B-1422/ JCM 16871 / LMG 4051 / NBRC 15346 /
Gene: bphP, DR_A0050 / Plasmid: PET21B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical
ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: small flakes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 12% polyethylene glycol (PEG) 3350, 200 mM ammonium acetate, 5% fructose, 5% glucose, and 100 mM sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 88343 / % possible obs: 98.8 % / Redundancy: 3.292 % / CC1/2: 0.989 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.181 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.363.2591.49664830.3251.79299.2
2.36-2.51.17128760.4291.40498.6
2.5-2.80.678197790.7020.80499.1
2.8-30.37391230.8960.44799.2
3-40.149230790.9780.17798.9
4-60.082118610.9840.09898.2
6-100.06739880.9920.08198.4
10-500.06411540.9930.07898.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.88 Å45.99 Å
Translation5.88 Å45.99 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5B

5k5b


Resolution: 2.3→45.99 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.668 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26819 4418 5 %RANDOM
Rwork0.235 ---
obs0.23667 83924 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.392 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20.52 Å2
2---0.02 Å2-0 Å2
3----2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14041 0 172 426 14639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214674
X-RAY DIFFRACTIONr_bond_other_d0.0030.01613456
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.66820105
X-RAY DIFFRACTIONr_angle_other_deg0.3621.56731281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28951844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.1375112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.018102155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0460.22270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022753
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_it2.7165.1947409
X-RAY DIFFRACTIONr_mcbond_other2.7145.1947409
X-RAY DIFFRACTIONr_mcangle_it4.4017.7729239
X-RAY DIFFRACTIONr_mcangle_other4.4017.7729240
X-RAY DIFFRACTIONr_scbond_it2.8155.5427265
X-RAY DIFFRACTIONr_scbond_other2.8155.5427265
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.588.210866
X-RAY DIFFRACTIONr_long_range_B_refined7.55372.39716337
X-RAY DIFFRACTIONr_long_range_B_other7.5572.20216257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 323 -
Rwork0.366 6133 -
obs--99.17 %

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