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- PDB-6g1y: Crystal structure of the photosensory core module (PCM) of a bath... -

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Basic information

Entry
Database: PDB / ID: 6g1y
TitleCrystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state.
Components(Bacteriophytochrome protein) x 2
KeywordsSIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / PFR STATE / LIGHT ADAPTATION / BATHY PHYTOCHROME / METHYLATION / PHOTOSENSORY CORE MODULE
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 / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold ...Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / 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 / Beta-Lactamase / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EL5 / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchmidt, A. / Qureshi, B.M. / Scheerer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
SFB1078 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural snapshot of a bacterial phytochrome in its functional intermediate state.
Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / ...Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / Krauss, N. / Lamparter, T. / Hildebrandt, P. / Scheerer, P.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _struct_ncs_dom_lim.beg_auth_comp_id ..._chem_comp.pdbx_synonyms / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1634
Polymers112,9932
Non-polymers1,1692
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.520, 93.360, 174.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISVALVALAA7 - 807 - 80
21HISHISVALVALBB7 - 807 - 80
12ARGARGGLUGLUAA86 - 50186 - 501
22ARGARGGLUGLUBB86 - 50186 - 501

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998444, 0.032186, 0.045546), (-0.042393, -0.968643, -0.244815), (0.036239, -0.246365, 0.968499)36.13307, 230.75047, 27.80574

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Components

#1: Protein Bacteriophytochrome protein


Mass: 56490.199 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: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81
#2: Protein Bacteriophytochrome protein


Mass: 56503.223 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: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: MPD, VAPOR DIFFUSION, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2015 / Details: MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→45.09 Å / Num. obs: 42806 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.187 / Net I/σ(I): 8.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.622 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2W

3c2w


Resolution: 2.5→45.09 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.656 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2050 4.8 %RANDOM
Rwork0.201 ---
obs0.203 40755 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--1.36 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 86 202 7966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028039
X-RAY DIFFRACTIONr_angle_refined_deg1.31.96910931
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11111loose positional0.375
26157loose positional0.225
11111loose thermal8.8610
26157loose thermal3.6110
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 134 -
Rwork0.316 2966 -
obs--99.9 %
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)
10.90160.18580.8670.22660.07141.17650.0384-0.0329-0.03980.01250.0178-0.02230.05920.1106-0.05620.102-0.0151-0.00210.1383-0.01680.005325.968134.034231.5973
20.72780.275-0.39920.42080.09721.26860.0454-0.06670.00020.0231-0.02330.075-0.0424-0.186-0.02210.07010.00840.00450.15860.02280.025314.570792.533626.8937
30.21650.00630.30980.66040.52561.58410.04170.06780.0057-0.0527-0.0009-0.0101-0.05950.1017-0.04080.05940.00990.00320.11640.00610.003514.025136.2292-7.7165
40.29870.1129-0.26390.8099-0.70181.27690.04360.0821-0.0034-0.0714-0.0141-0.00480.0349-0.1033-0.02950.08060.035-0.00880.12430.0010.003325.957899.6968-12.0746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 306
2X-RAY DIFFRACTION2B6 - 306
3X-RAY DIFFRACTION3A307 - 503
4X-RAY DIFFRACTION4B307 - 503

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