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- PDB-6r27: Crystallographic superstructure of the photosensory core module (... -

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Basic information

Entry
Database: PDB / ID: 6r27
TitleCrystallographic superstructure of the 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 / metal ion binding
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. / His Kinase A (phospho-acceptor) domain ...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. / 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: 3.4 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: Bacteriophytochrome protein
C: Bacteriophytochrome protein
D: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,2478
Polymers225,8524
Non-polymers2,3954
Water00
1
A: Bacteriophytochrome protein
B: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1234
Polymers112,9262
Non-polymers1,1972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-27 kcal/mol
Surface area39810 Å2
MethodPISA
2
C: Bacteriophytochrome protein
D: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1234
Polymers112,9262
Non-polymers1,1972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-27 kcal/mol
Surface area41130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.218, 240.218, 160.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLEULEUAA20 - 49920 - 499
21CYSCYSLEULEUBB20 - 49920 - 499
12SERSERVALVALAA19 - 49819 - 498
22SERSERVALVALCC19 - 49819 - 498
13CYSCYSLEULEUAA20 - 49920 - 499
23CYSCYSLEULEUDD20 - 49920 - 499
14CYSCYSLEULEUBB20 - 49920 - 499
24CYSCYSLEULEUCC20 - 49920 - 499
15CYSCYSLEULEUBB20 - 49920 - 499
25CYSCYSLEULEUDD20 - 49920 - 499
16CYSCYSGLUGLUCC20 - 50320 - 503
26CYSCYSGLUGLUDD20 - 50320 - 503

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Bacteriophytochrome protein


Mass: 56463.027 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C34H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
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: 2.6 Å3/Da / Density % sol: 52.65 % / Description: tetragonal prism
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 20% Sucrose as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.4→47.89 Å / Num. obs: 32444 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 68.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.079 / Rrim(I) all: 0.128 / Χ2: 0.95 / Net I/σ(I): 10.5
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4659 / CC1/2: 0.87 / Rpim(I) all: 0.341 / Rrim(I) all: 0.557 / Χ2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSNov 1, 2016data reduction
Aimless0.7.2data scaling
PHASER2.3.0phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSQ

5hsq


Resolution: 3.4→47.89 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.859 / SU B: 86.901 / SU ML: 0.613 / Cross valid method: THROUGHOUT / ESU R Free: 0.717 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29701 1578 5 %RANDOM
Rwork0.25497 ---
obs0.25713 29735 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13946 0 176 0 14122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01314439
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713158
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.64719685
X-RAY DIFFRACTIONr_angle_other_deg1.1041.5830276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95151863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53621.642676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.801152019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9041596
X-RAY DIFFRACTIONr_chiral_restr0.0450.21877
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023067
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_it1.2434.2557491
X-RAY DIFFRACTIONr_mcbond_other1.2434.2557490
X-RAY DIFFRACTIONr_mcangle_it2.2216.3759341
X-RAY DIFFRACTIONr_mcangle_other2.2216.3759342
X-RAY DIFFRACTIONr_scbond_it0.9924.3486948
X-RAY DIFFRACTIONr_scbond_other0.9924.3496949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7876.50210345
X-RAY DIFFRACTIONr_long_range_B_refined4.78349.86315687
X-RAY DIFFRACTIONr_long_range_B_other4.78249.86815688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A138280.07
12B138280.07
21A138240.08
22C138240.08
31A131980.07
32D131980.07
41B132270.09
42C132270.09
51B130520.08
52D130520.08
61C129820.08
62D129820.08
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 127 -
Rwork0.33 2208 -
obs--98.98 %
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)
14.37842.30170.82013.0702-0.52125.7348-0.29730.20950.3105-0.28610.04140.1708-0.29370.23680.2560.55120.0791-0.03490.2021-0.04230.193646.452820.128982.1156
21.87150.13420.68662.1341-0.85811.92930.004-0.21760.29350.1446-0.15360.03040.0508-0.11770.14960.7224-0.00440.11440.3899-0.13480.11443.59996.6987100.1665
33.2539-0.6917-0.45044.25440.46680.559-0.0407-0.2256-0.2955-0.183-0.098-0.29270.051-0.22830.13870.5880.0380.13640.470.05650.126842.5355-29.7649106.4847
45.9651-4.2861-0.13277.5759-1.09713.7194-0.1269-0.05360.73210.885-0.1585-0.499-0.60150.22670.28540.648-0.3537-0.18920.28050.02790.240679.412619.2594117.3789
52.01770.45010.39662.84091.40322.0188-0.06790.11020.03480.2792-0.2692-0.1273-0.17380.23460.33710.623-0.2828-0.14860.48450.2040.141479.38855.712499.6874
64.64020.2968-0.88715.2696-1.1710.5525-0.13030.47-0.30580.4497-0.00710.18590.05550.09910.13740.559-0.03930.17340.549-0.06610.147579.0322-30.207594.7436
74.15672.15151.08314.01621.54975.668-0.1020.2555-0.44440.0134-0.1526-0.14380.4015-0.02010.25460.51270.05520.02150.25260.01460.123873.6594-20.0947123.1004
81.3178-0.502-0.73843.18230.82621.628-0.0169-0.0852-0.03160.5827-0.18610.0057-0.1890.25270.20310.6697-0.1426-0.14480.30550.04990.050575.4941-5.8672141.0552
94.018-2.0071-0.22172.97060.96110.6759-0.4282-0.22790.1645-0.22040.19090.5269-0.07890.19820.23730.87250.0716-0.38240.4051-0.08860.290270.404931.6283152.424
103.3515-2.35991.36434.01871.4284.58-0.2989-0.1955-0.01080.1607-0.02860.03791.0006-0.63760.32740.8964-0.36960.21480.4488-0.04260.06538.5141-18.1221156.9861
111.16040.7862-1.50613.22-0.36343.2299-0.38380.1166-0.0452-0.56310.2289-0.26270.3465-0.74740.15490.7449-0.35820.00630.6812-0.1170.051539.9831-4.4059139.3382
123.30431.66690.59113.4126-0.0670.9987-0.23660.5690.17380.49720.2771-0.7010.1244-0.2817-0.04050.8243-0.065-0.40850.40960.08970.330148.731533.4437129.2636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 123
2X-RAY DIFFRACTION2A124 - 308
3X-RAY DIFFRACTION3A309 - 499
4X-RAY DIFFRACTION4B20 - 123
5X-RAY DIFFRACTION5B124 - 308
6X-RAY DIFFRACTION6B309 - 499
7X-RAY DIFFRACTION7C19 - 123
8X-RAY DIFFRACTION8C124 - 308
9X-RAY DIFFRACTION9C309 - 503
10X-RAY DIFFRACTION10D20 - 123
11X-RAY DIFFRACTION11D124 - 308
12X-RAY DIFFRACTION12D309 - 503

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