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- PDB-4y3i: PAS-GAF fragment from Deinococcus radiodurans BphP assembled with... -

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Basic information

Entry
Database: PDB / ID: 4y3i
TitlePAS-GAF fragment from Deinococcus radiodurans BphP assembled with BV - Y307S, low dose
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / low-dose / spectroscopy / bilin chromophore / phythochrome
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 / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain ...: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / 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 / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / PAS domain superfamily / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLi, F. / Burgie, E.S. / Yu, T. / Heroux, A. / Schatz, G.C. / Vierstra, R.D. / Orville, A.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)8P41GM103473-16 United States
Department of Energy (DOE, United States)FWP BO-70 United States
National Science Foundation (NSF, United States)MCB-1329956 United States
National Science Foundation (NSF, United States)CHE-1147335 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome.
Authors: Li, F. / Burgie, E.S. / Yu, T. / Heroux, A. / Schatz, G.C. / Vierstra, R.D. / Orville, A.M.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 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_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
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)35,0492
Polymers34,4631
Non-polymers5861
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area14140 Å2
Unit cell
Length a, b, c (Å)89.481, 51.917, 80.339
Angle α, β, γ (deg.)90.00, 116.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein / bilin chromophore


Mass: 34463.324 Da / Num. of mol.: 1 / Fragment: PAS-GAF fragment (UNP residues 4-321) / Mutation: Y307S
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)
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


Mass: 18.015 Da / Num. of mol.: 119 / 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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% isopropanol, 19% PEG3350, 5% glycerol, 100 mM citric acid/NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2013 / Details: multi-crystals for low dose
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 34408 / % possible obs: 97.9 % / Redundancy: 5.3 % / Net I/σ(I): 21.4
Reflection shellResolution: 1.694→1.738 Å / Redundancy: 3 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.8 / % possible all: 80.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 209C

209c


Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.153 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22614 1809 5 %RANDOM
Rwork0.19021 ---
obs0.19206 34408 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.01 Å2
2--0.96 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 43 119 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192653
X-RAY DIFFRACTIONr_bond_other_d2.6470.025
X-RAY DIFFRACTIONr_angle_refined_deg2.3631.9993657
X-RAY DIFFRACTIONr_angle_other_deg10.991311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14923.717113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9181519
X-RAY DIFFRACTIONr_chiral_restr0.1880.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0222056
X-RAY DIFFRACTIONr_gen_planes_other0.0170.022
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_it2.3392.0371298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4553.0481627
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.742.2081355
X-RAY DIFFRACTIONr_scbond_other2.7372.2081354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9213.2452024
X-RAY DIFFRACTIONr_long_range_B_refined5.86817.3044024
X-RAY DIFFRACTIONr_long_range_B_other5.86817.3054025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.694→1.738 Å
RfactorNum. reflection% reflection
Rfree0.278 109 5 %
Rwork0.222 2108 -
obs--80.82 %

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