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- PDB-9g8c: Crystal structure of the photosensory core module (PCM) of a cyan... -

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Basic information

Entry
Database: PDB / ID: 9g8c
TitleCrystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF165 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.
Components(histidine kinase) x 2
KeywordsSIGNALING PROTEIN / fluorescent protein / phytochrome / bacteriophytochrome / Pfr-state / ortho-cyano-phenylalanine / Stark labels
Function / homology
Function and homology information


protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region ...Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-EL5 / DI(HYDROXYETHYL)ETHER / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSauthof, L. / Schmidt, A. / Scheerer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1078 - project number 221545957 - subproject B06 Germany
German Research Foundation (DFG)EXC 311 2008/1 - UniSysCat - 390540038 - Research Unit E Germany
CitationJournal: J.Phys.Chem.B / Year: 2024
Title: Hydrogen Bonding and Noncovalent Electric Field Effects in the Photoconversion of a Phytochrome.
Authors: Nguyen, A.D. / Michael, N. / Sauthof, L. / von Sass, J. / Hoang, O.T. / Schmidt, A. / La Greca, M. / Schlesinger, R. / Budisa, N. / Scheerer, P. / Mroginski, M.A. / Kraskov, A. / Hildebrandt, P.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,76615
Polymers113,1942
Non-polymers2,57213
Water17,258958
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-34 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.723, 93.764, 174.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein histidine kinase


Mass: 56603.371 Da / Num. of mol.: 1 / Mutation: Y165oCNF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81, histidine kinase
#2: Protein histidine kinase


Mass: 56590.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81, histidine kinase

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Non-polymers , 6 types, 971 molecules

#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EL5 / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid / biliverdin, bound form at Pfr state


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 958 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 279 K / Method: vapor diffusion
Details: 30 - 40% MPD, 5 - 15% PEG 8000, 0.1 M MES pH 5.5 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.9→45.95 Å / Num. obs: 96932 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6544 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.983 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 4853 5 %RANDOM
Rwork0.18524 ---
obs0.18714 92138 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--1.84 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7503 0 158 958 8619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138004
X-RAY DIFFRACTIONr_bond_other_d0.0090.0157586
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.64710871
X-RAY DIFFRACTIONr_angle_other_deg1.3551.57617429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13451015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.75120.429420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.502151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5211561
X-RAY DIFFRACTIONr_chiral_restr0.0640.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028986
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021820
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_it1.5032.5173938
X-RAY DIFFRACTIONr_mcbond_other1.5012.5163937
X-RAY DIFFRACTIONr_mcangle_it2.3583.7614910
X-RAY DIFFRACTIONr_mcangle_other2.3583.7624911
X-RAY DIFFRACTIONr_scbond_it1.8332.7274066
X-RAY DIFFRACTIONr_scbond_other1.8332.7264067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9633.9985934
X-RAY DIFFRACTIONr_long_range_B_refined5.14130.9149112
X-RAY DIFFRACTIONr_long_range_B_other4.93930.2678853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 337 -
Rwork0.296 6544 -
obs--97.19 %

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