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- PDB-8co5: The surface-engineered photosensory module (PAS-GAF-PHY) of the b... -

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Basic information

Entry
Database: PDB / ID: 8co5
TitleThe surface-engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form with parallel dimer formation
ComponentsBacteriophytochrome protein
KeywordsSIGNALING PROTEIN / BILIN CHROMOPHORE / PARALLEL DIMER / PHYTOCHROME / PHOTORECEPTOR
Function / homology
Function and homology information


red or far-red light photoreceptor activity / red, far-red light phototransduction / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
: / 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 ...: / 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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
: / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSchmidt, A. / Sauthof, L. / Krauss, N. / Scheerer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1078 Germany
CitationJournal: To Be Published
Title: Crystal structures of a bacterial phytochrome exhibiting a group-subgroup relationship reveal pronounced flexibility of the photosensory core module in the Pr state
Authors: Scheerer, P. / Schmidt, A. / Nagano, S. / Qureshi, B.M. / Szczepek, M. / Sauthof, L. / Michael, N. / Inomata, K. / Lamparter, T. / Krauss, N.
History
DepositionFeb 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3483
Polymers54,7371
Non-polymers6112
Water1,49583
1
A: Bacteriophytochrome protein
hetero molecules

A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6966
Polymers109,4742
Non-polymers1,2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area1820 Å2
ΔGint-34 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.477, 172.477, 78.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-756-

HOH

21A-779-

HOH

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Components

#1: Protein Bacteriophytochrome protein


Mass: 54736.945 Da / Num. of mol.: 1 / Mutation: E77A, E78A, E327A, K328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Strain: C58 / Gene: Atu1990 / Plasmid: PET21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7CY45
#2: Chemical ChemComp-V8U / 3-[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-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.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 10-20% PEG4000, 100mM Tris buffer, 0.2M MgCl2 / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.42→46.49 Å / Num. obs: 22938 / % possible obs: 99.94 % / Redundancy: 8.6 % / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 2.42→2.51 Å / Num. unique obs: 2361 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→46.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 25.704 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25195 1159 5.1 %RANDOM
Rwork0.21209 ---
obs0.21408 21783 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.42→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 44 83 3644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0747.1421903
X-RAY DIFFRACTIONr_mcbond_other2.0987.141902
X-RAY DIFFRACTIONr_mcangle_it3.04710.7012375
X-RAY DIFFRACTIONr_mcangle_other3.07110.7032376
X-RAY DIFFRACTIONr_scbond_it1.6687.0861760
X-RAY DIFFRACTIONr_scbond_other1.6687.0861761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.48710.5872623
X-RAY DIFFRACTIONr_long_range_B_refined4.59983.0724066
X-RAY DIFFRACTIONr_long_range_B_other4.59983.0644067
X-RAY DIFFRACTIONr_rigid_bond_restr6.78537032
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 89 -
Rwork0.323 1566 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 27.936 Å / Origin y: 32.998 Å / Origin z: 20.873 Å
111213212223313233
T0.0431 Å2-0.0029 Å20.0006 Å2-0.0455 Å2-0.0025 Å2--0.001 Å2
L0.1347 °2-0.1243 °20.1031 °2-0.1407 °2-0.1056 °2--0.0986 °2
S0.0075 Å °0.0082 Å °-0.0029 Å °-0.0107 Å °-0.0083 Å °-0.0016 Å °0.0089 Å °0.0058 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 306
2X-RAY DIFFRACTION1A307 - 502

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