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- PDB-6r26: The photosensory core module (PAS-GAF-PHY) of the bacterial phyto... -

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Basic information

Entry
Database: PDB / ID: 6r26
TitleThe photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state
ComponentsBacteriophytochrome protein
KeywordsSIGNALING PROTEIN / photoreceptor / bilin protein / locked chromophore / crystallographic superstructure
Function / homology
Function and homology information


red or far-red light photoreceptor activity / red, far-red light phototransduction / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / regulation of DNA-templated transcription ...red or far-red light photoreceptor activity / red, far-red light phototransduction / protein histidine kinase activity / osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Histidine kinase/HSP90-like ATPase ...Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Histidine kinase/HSP90-like ATPase / 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 / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-JQ2 / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsScheerer, P. / Michael, N. / Lamparter, T. / Krauss, N.
Funding support Germany, 6items
OrganizationGrant numberCountry
German Research FoundationSFB498-B2 Germany
German Research FoundationSFB1078-B6 Germany
German Research FoundationLA 799/18-1 Germany
German Research FoundationKR 2034/1-1 Germany
German Research FoundationDFG under Germanys Excellence Strategy - UniSysCat - 390540038 Germany
German Research FoundationDFG Cluster of Excellence - UniCat Germany
Citation
Journal: To Be Published
Title: Crystal structures of the photosensory core module of bacteriophytochrome Agp1 reveal pronounced structural flexibility of this protein in the red-absorbing Pr state
Authors: Scheerer, P. / Schmidt, A. / Nagano, S. / Qureshi, B. / Szczepek, M. / Sauthof, L. / Michael, N. / Inomata, K. / Lamparter, T. / Krauss, N.
#1: Journal: J. Struct. Biol. / Year: 2006
Title: Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens.
Authors: Scheerer, P. / Michael, N. / Park, J.H. / Noack, S. / Foerster, C. / Hammam, M.A. / Inomata, K. / Choe, H.W. / Lamparter, T. / Krauss, N.
#2: Journal: J. Biol. Chem. / Year: 2016
Title: The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.
Authors: Nagano, S. / Scheerer, P. / Zubow, K. / Michael, N. / Inomata, K. / Lamparter, T. / Krauss, N.
History
DepositionMar 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1023
Polymers56,4631
Non-polymers6392
Water00
1
A: Bacteriophytochrome protein
hetero molecules

A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2046
Polymers112,9262
Non-polymers1,2784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area2020 Å2
ΔGint-38 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.445, 174.445, 79.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Bacteriophytochrome protein


Mass: 56463.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu1990 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1blue / References: UniProt: Q7CY45
#2: Chemical ChemComp-JQ2 / 3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 598.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20-23% PEG 3350, 50 mM NaCl and 100 mM Tris/Cl, in 30% PEG 3350 as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 3.11→46.84 Å / Num. obs: 11232 / % possible obs: 99.3 % / Redundancy: 9.4 % / Biso Wilson estimate: 95.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Net I/σ(I): 16.3
Reflection shellResolution: 3.11→3.32 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5 / Num. unique obs: 1987 / CC1/2: 0.962 / Rpim(I) all: 0.175 / Rrim(I) all: 0.397 / Χ2: 0.62 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSNov 1, 2016data reduction
Aimless0.7.4data scaling
PHASER2.7.17phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I5L

5i5l


Resolution: 3.11→46.84 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 47.757 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27618 589 5.2 %RANDOM
Rwork0.21564 ---
obs0.21895 10642 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 103.842 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å2-0 Å20 Å2
2--2.59 Å2-0 Å2
3----5.18 Å2
Refinement stepCycle: LAST / Resolution: 3.11→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 45 0 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133612
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173198
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.6454939
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5797350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29221.863161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91415466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7771521
X-RAY DIFFRACTIONr_chiral_restr0.0430.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
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_it2.3437.6781914
X-RAY DIFFRACTIONr_mcbond_other2.3417.6781913
X-RAY DIFFRACTIONr_mcangle_it3.86811.5182389
X-RAY DIFFRACTIONr_mcangle_other3.86711.5192390
X-RAY DIFFRACTIONr_scbond_it2.4387.8521698
X-RAY DIFFRACTIONr_scbond_other2.4387.8541699
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.97711.7022551
X-RAY DIFFRACTIONr_long_range_B_refined6.52592.4673973
X-RAY DIFFRACTIONr_long_range_B_other6.52892.4843974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.106→3.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 37 -
Rwork0.245 761 -
obs--96.84 %
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)
18.3946-0.71420.24742.36420.96073.17440.2899-0.3642-0.5634-0.0346-0.1164-0.08730.28140.4372-0.17350.19180.09140.00740.14270.05060.16847.27218.00938.754
24.5408-3.15920.59485.2796-2.46422.59990.96591.05-0.5581-1.0764-1.0870.35620.45140.28440.12110.33740.2729-0.1470.2956-0.15410.150134.83924.11320.609
34.3796-3.35683.46693.9624-3.71363.62460.0320.66211.4056-0.3154-0.8938-0.82840.23660.64880.86180.15060.1128-0.03430.55260.24840.549523.55154.11612.24
45.5367-1.82713.70743.6229-2.06184.79380.5604-0.5237-0.6487-0.0377-0.01060.45060.2089-0.714-0.54990.1642-0.0371-0.12980.53030.08550.33893.01650.49311.488
53.4597-3.11172.00395.7088-2.48572.37380.56840.29-0.5759-0.4374-0.29361.21370.6250.2259-0.27480.38820.1546-0.18130.6137-0.12770.478914.9340.4613.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 124
2X-RAY DIFFRACTION2A125 - 288
3X-RAY DIFFRACTION3A289 - 365
4X-RAY DIFFRACTION4A366 - 443
5X-RAY DIFFRACTION5444 - 502

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