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- PDB-4zrr: Crystal Structure of Monomeric Bacteriophytochrome mutant D207L Y... -

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Basic information

Entry
Database: PDB / ID: 4zrr
TitleCrystal Structure of Monomeric Bacteriophytochrome mutant D207L Y263F at 1.5 A resolution Using a home source.
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / BACTERIOPHYTOCHROME / PAS / GAF / BILIVERDIN / SIGNALING PROTEIN
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator 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. / Signal transduction histidine kinase-related protein, C-terminal ...: / 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. / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / Chem-LBW / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBhattacharya, S. / Satyshur, K.A. / Lehtivuori, H. / Forest, K.T.
Funding support Finland, United States, 6items
OrganizationGrant numberCountry
Academy of Finland277194 Finland
Fulbright Center in Finland Finland
University of Wisconsin-MadisonPRJ79XE United States
W.H. Peterson Fellowship United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P1000817 United States
CitationJournal: Front Mol Biosci / Year: 2015
Title: Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor.
Authors: Lehtivuori, H. / Bhattacharya, S. / Angenent-Mari, N.M. / Satyshur, K.A. / Forest, K.T.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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
Revision 1.4Nov 6, 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: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6626
Polymers37,1831
Non-polymers1,4795
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.819, 55.046, 69.797
Angle α, β, γ (deg.)90.00, 91.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37183.344 Da / Num. of mol.: 1 / Mutation: F145S,D207L, Y263F, L311E, L314E
Source method: isolated from a genetically manipulated source
Details: T7 Expression vector is on the N-terminal end and is present in the crystallized protein but not seen.
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9RZA4, histidine kinase

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Non-polymers , 5 types, 293 molecules

#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: Chemical ChemComp-LBW / 3-[2-[(Z)-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E,4R)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 51.62 % / Description: Green prismatic crystals.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Feb 14, 2015
RadiationMonochromator: Goebel Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→47.6 Å / Num. obs: 54864 / % possible obs: 96 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.84 Å2 / Rsym value: 0.05 / Net I/σ(I): 14.69
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.83 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8G

4o8g


Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.403 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2709 4.9 %RANDOM
Rwork0.16 ---
obs0.162 52043 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.03 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 105 288 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192641
X-RAY DIFFRACTIONr_bond_other_d0.0020.022581
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.0193627
X-RAY DIFFRACTIONr_angle_other_deg1.0263.0015865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31723.019106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07815391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5711521
X-RAY DIFFRACTIONr_chiral_restr0.1230.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213002
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02589
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_it1.11.6631289
X-RAY DIFFRACTIONr_mcbond_other1.0961.6611288
X-RAY DIFFRACTIONr_mcangle_it1.3982.4921625
X-RAY DIFFRACTIONr_mcangle_other1.3982.4941626
X-RAY DIFFRACTIONr_scbond_it1.1991.9051352
X-RAY DIFFRACTIONr_scbond_other1.1991.9061353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3942.7661999
X-RAY DIFFRACTIONr_long_range_B_refined2.5914.5613082
X-RAY DIFFRACTIONr_long_range_B_other2.5914.5663083
X-RAY DIFFRACTIONr_rigid_bond_restr0.99935222
X-RAY DIFFRACTIONr_sphericity_free27.097561
X-RAY DIFFRACTIONr_sphericity_bonded6.54355370
LS refinement shellResolution: 1.51→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 174 -
Rwork0.188 3362 -
obs--84.45 %

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