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- PDB-5oy5: Monomeric crystal structure of RpBphP1 photosensory core domain f... -

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Basic information

Entry
Database: PDB / ID: 5oy5
TitleMonomeric crystal structure of RpBphP1 photosensory core domain from the bacterium Rhodopseudomonas palustris
ComponentsBphP1
KeywordsPHOTOSYNTHESIS / Bacteriophytochrome / Gene Repressor / Biliverdin
Function / homology
Function and homology information


detection of visible light / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / BphP1
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPapiz, M.Z. / Bellini, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/E002609/2 United Kingdom
STFC Darebury Laboratory United Kingdom
Citation
Journal: To Be Published
Title: Insights into the light-induced molecular switch of the bacteriophytochrome RpBphP1 probed by SAXS, modelling and UV-Vis optical properties
Authors: Papiz, M.Z. / Bellini, D.
#1: Journal: Structure / Year: 2012
Title: Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.
Authors: Bellini, D. / Papiz, M.Z.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BphP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3552
Polymers57,7731
Non-polymers5831
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-19 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.780, 92.780, 449.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein BphP1


Mass: 57772.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A161I5N6
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 5.07 Å3/Da / Density % sol: 75.77 % / Description: Bipyramid 0.6 mm
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4% PGA (poly-gamma-glutamic acid polymer), 200 mM KBr and 100 mM TrisHCl pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2010
Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→79 Å / Num. obs: 34645 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 11 % / Rsym value: 0.062 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 12 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2758 / Rsym value: 0.62 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW9

4gw9


Resolution: 2.6→79.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.214 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1840 5 %RANDOM
Rwork0.19162 ---
obs0.19408 34645 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å2-0 Å2
2---0.29 Å2-0 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.6→79.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 43 218 4057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9765348
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6545490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64222.784176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.12715619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1531539
X-RAY DIFFRACTIONr_chiral_restr0.1490.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0213024
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.7033.121963
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9394.6722452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7853.3981964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined18.03244.5046147
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 133 -
Rwork0.342 2490 -
obs--99.62 %
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)
11.6810.80530.19092.67930.16553.40070.0393-0.3023-0.1080.3593-0.1673-0.13230.004-0.06880.1280.5413-0.0587-0.0070.12940.04590.02719.166-2.92118.026
23.37740.95552.74472.28472.19746.80190.0011-0.2605-0.1932-0.24860.1985-0.3546-1.22540.8913-0.19960.9417-0.57850.13840.45620.01460.218228.63422.55439.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 340
2X-RAY DIFFRACTION2A341 - 507

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