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- PDB-3s7o: Crystal Structure of the Infrared Fluorescent D207H variant of De... -

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Basic information

Entry
Database: PDB / ID: 3s7o
TitleCrystal Structure of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 1.24 angstrom resolution
ComponentsBacteriophytochrome
KeywordsFLUORESCENT PROTEIN / BILIVERDIN / PAS / GAF / Phytochrome / bacteriophytochrome / Photoreceptor
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 / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsForest, K.T. / Auldridge, M.E. / Satyshur, K.A. / Anstrom, D.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein.
Authors: Auldridge, M.E. / Satyshur, K.A. / Anstrom, D.M. / Forest, K.T.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 17, 2014Group: Atomic model
Revision 1.3Sep 13, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8543
Polymers37,1761
Non-polymers6782
Water6,575365
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7086
Polymers74,3532
Non-polymers1,3564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5330 Å2
ΔGint-39 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.848, 51.302, 80.363
Angle α, β, γ (deg.)90.00, 115.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37176.418 Da / Num. of mol.: 1 / Fragment: Chromophore binidng domain (UNP Residues 1-321) / Mutation: D207H Y307S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: mother liquor: 20% v/v PEG 4000, 20% v/v isopropanol, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.24→25 Å / Num. all: 87959 / Num. obs: 84232 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.47
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.32 / % possible all: 79.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 1.24→24.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.335 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17505 4403 5 %RANDOM
Rwork0.15301 ---
obs0.15407 83531 97.24 %-
all-84232 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.05 Å2
2---0.06 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.144 Å
Refinement stepCycle: LAST / Resolution: 1.24→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 49 365 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222670
X-RAY DIFFRACTIONr_bond_other_d0.0020.021785
X-RAY DIFFRACTIONr_angle_refined_deg1.5062.0093675
X-RAY DIFFRACTIONr_angle_other_deg2.29134371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91622.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.631521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213015
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02524
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_it1.5311.51676
X-RAY DIFFRACTIONr_mcbond_other2.0811.5659
X-RAY DIFFRACTIONr_mcangle_it2.66522725
X-RAY DIFFRACTIONr_scbond_it3.1273994
X-RAY DIFFRACTIONr_scangle_it5.0474.5949
X-RAY DIFFRACTIONr_rigid_bond_restr1.4534455
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 237 -
Rwork0.237 4866 -
obs--76.84 %

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