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- PDB-6ftd: Deinococcus radiodurans BphP PAS-GAF H290T mutant -

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Basic information

Entry
Database: PDB / ID: 6ftd
TitleDeinococcus radiodurans BphP PAS-GAF H290T mutant
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. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS 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. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEdlund, P. / Takala, H. / Westenhoff, S. / Ihalainen, J.A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Research Council Sweden
CitationJournal: Phys Chem Chem Phys / Year: 2018
Title: Coordination of the biliverdin D-ring in bacteriophytochromes.
Authors: Lenngren, N. / Edlund, P. / Takala, H. / Stucki-Buchli, B. / Rumfeldt, J. / Peshev, I. / Hakkanen, H. / Westenhoff, S. / Ihalainen, J.A.
History
DepositionFeb 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14712
Polymers74,3852
Non-polymers1,76210
Water10,323573
1
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0736
Polymers37,1921
Non-polymers8815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0736
Polymers37,1921
Non-polymers8815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.810, 53.030, 135.880
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37192.410 Da / Num. of mol.: 2 / Mutation: H290T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: pET21B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: 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.: 2 / Source method: obtained synthetically / Formula: C33H37N4O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.95
Details: 67 mM Sodium acetate, 3.3 % PEG400, 1mM DTT, 30% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→47.33 Å / Num. obs: 132351 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.25 % / Biso Wilson estimate: 15.679 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.124 / Net I/σ(I): 7.48
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 4.26 % / Rmerge(I) obs: 1.362 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 9607 / CC1/2: 0.336 / Rrim(I) all: 1.552 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSMarch 1, 2015data reduction
XSCALEdata scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5B

5k5b


Resolution: 1.4→47.33 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.467 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19816 6620 5 %RANDOM
Rwork0.14795 ---
obs0.15046 125781 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.41 Å2
2--0.06 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.4→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 126 573 5489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0195327
X-RAY DIFFRACTIONr_bond_other_d0.0020.025133
X-RAY DIFFRACTIONr_angle_refined_deg2.5512.0077344
X-RAY DIFFRACTIONr_angle_other_deg1.219311810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79523.396212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6571539
X-RAY DIFFRACTIONr_chiral_restr0.1550.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216125
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021164
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_it4.7452.0842662
X-RAY DIFFRACTIONr_mcbond_other4.7192.082658
X-RAY DIFFRACTIONr_mcangle_it5.4013.13360
X-RAY DIFFRACTIONr_mcangle_other5.43.1023361
X-RAY DIFFRACTIONr_scbond_it5.5692.5582665
X-RAY DIFFRACTIONr_scbond_other5.5692.5582665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.163.6823975
X-RAY DIFFRACTIONr_long_range_B_refined6.36818.8536290
X-RAY DIFFRACTIONr_long_range_B_other6.11218.2585980
X-RAY DIFFRACTIONr_rigid_bond_restr5.167310460
X-RAY DIFFRACTIONr_sphericity_free32.0825124
X-RAY DIFFRACTIONr_sphericity_bonded13.416510750
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 485 -
Rwork0.411 9227 -
obs--99.48 %

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