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- PDB-5mg1: Structure of the photosensory module of Deinococcus phytochrome b... -

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Basic information

Entry
Database: PDB / ID: 5mg1
TitleStructure of the photosensory module of Deinococcus phytochrome by serial femtosecond X-ray crystallography
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Photosensory module / phytochrome / biliverdin / photoreceptor
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
PHY domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / PAS domain ...PHY domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsBurgie, E.S. / Fuller, F.D. / Gul, S. / Young, I.D. / Brewster, A.S. / Clinger, J. / Andi, B. / Stan, C. / Allaire, M. / Nelsen, S. ...Burgie, E.S. / Fuller, F.D. / Gul, S. / Young, I.D. / Brewster, A.S. / Clinger, J. / Andi, B. / Stan, C. / Allaire, M. / Nelsen, S. / Alonso-Mori, R. / Phillips Jr., G.N. / Sauter, N.K. / Kern, J. / Yachandra, V.K. / Yano, J. / Vierstra, R.D. / Orville, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science FoundationMCB-1329956 United States
CitationJournal: Nat. Methods / Year: 2017
Title: Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.
Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. ...Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. / de Lichtenberg, C. / Hussein, R. / Pollock, C.J. / Zhang, M. / Stan, C.A. / Kroll, T. / Fransson, T. / Weninger, C. / Kubin, M. / Aller, P. / Lassalle, L. / Brauer, P. / Miller, M.D. / Amin, M. / Koroidov, S. / Roessler, C.G. / Allaire, M. / Sierra, R.G. / Docker, P.T. / Glownia, J.M. / Nelson, S. / Koglin, J.E. / Zhu, D. / Chollet, M. / Song, S. / Lemke, H. / Liang, M. / Sokaras, D. / Alonso-Mori, R. / Zouni, A. / Messinger, J. / Bergmann, U. / Boal, A.K. / Bollinger, J.M. / Krebs, C. / Hogbom, M. / Phillips, G.N. / Vierstra, R.D. / Sauter, N.K. / Orville, A.M. / Kern, J. / Yachandra, V.K. / Yano, J.
History
DepositionNov 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Nov 14, 2018Group: Data collection / Source and taxonomy / Category: diffrn / entity_src_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2802
Polymers56,6941
Non-polymers5861
Water1448
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5604
Polymers113,3882
Non-polymers1,1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area5260 Å2
ΔGint-36 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.700, 151.700, 151.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 56694.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.43 Å3/Da / Density % sol: 72.23 % / Description: 100 micron needles
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.5
Details: PEG 3350, Tacsimate pH 6.0, Tacsimate pH 7.0, ethylene glycol, PIPES-NaOH pH 6.5
Temp details: room temperature

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.305 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Oct 31, 2015 / Details: Compound refractive lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 3.3→131.376 Å / Num. obs: 15996 / % possible obs: 99.86 % / Redundancy: 39.16 % / CC1/2: 0.863 / Net I/σ(I): 29.234
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible all
8.9576-131.37666.96137.3190.833197.82
7.1096-8.957658.6478.0570.8371100
6.2108-7.109653.442.950.7721100
5.6429-6.210849.0735.5550.8171100
5.2384-5.642946.830.8290.7821100
4.9295-5.238444.933.2670.7711100
4.6826-4.929542.6532.2360.8421100
4.4788-4.682641.2733.5130.7111100
4.3064-4.478839.3629.170.8151100
4.1577-4.306437.8424.5610.7881100
4.0277-4.157736.5518.1050.67199.87
3.9126-4.027734.8914.0580.6571100
3.8096-3.912633.4811.5740.61100
3.7166-3.809632.388.4430.5681100
3.6321-3.716630.857.5690.3451100
3.5548-3.632129.316.4780.4211100
3.4837-3.554827.785.9520.3371100
3.418-3.483725.395.460.2321100
3.3569-3.41823.174.7050.2321100
3.3-3.356920.754.0690.178199.87

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.84 Å37.89 Å
Translation6.84 Å37.89 Å

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Processing

Software
NameVersionClassification
cctbx.xfeldata collection
cctbx.primedata reduction
cctbx.xfeldata reduction
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
psanadata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PAS-GAF from PDB 2O9C, and PHY domain from 4Q0J

2o9c

4q0j


Resolution: 3.3→37.894 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2447 820 5.14 %
Rwork0.2117 --
obs0.2135 15968 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.52 Å2 / Biso mean: 91.6934 Å2 / Biso min: 38.8 Å2
Refinement stepCycle: final / Resolution: 3.3→37.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 43 8 3777
Biso mean--71.4 63.88 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023917
X-RAY DIFFRACTIONf_angle_d0.5625370
X-RAY DIFFRACTIONf_chiral_restr0.038599
X-RAY DIFFRACTIONf_plane_restr0.004705
X-RAY DIFFRACTIONf_dihedral_angle_d17.3792344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.50660.34171230.299224542577
3.5066-3.77720.25761350.254124702605
3.7772-4.15680.27761520.221224622614
4.1568-4.75730.24051230.182125302653
4.7573-5.98990.22271230.20325512674
5.9899-37.89610.22141640.198926812845
Refinement TLS params.Method: refined / Origin x: -14.1022 Å / Origin y: 65.3452 Å / Origin z: 8.3921 Å
111213212223313233
T0.4655 Å2-0.1333 Å20.0186 Å2-0.7965 Å20.0335 Å2--0.5551 Å2
L1.1646 °2-0.9841 °20.4551 °2-2.1574 °2-0.7781 °2--2.0124 °2
S0.025 Å °-0.0933 Å °-0.0519 Å °0.1366 Å °-0.0909 Å °-0.1064 Å °-0.0993 Å °0.0643 Å °0.0619 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 6 through 550 )

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