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- PDB-3s7q: Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus... -

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Basic information

Entry
Database: PDB / ID: 3s7q
TitleCrystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain
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 / 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
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 ...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 / Chem-LBW / PHOSPHATE ION / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.748 Å
AuthorsAuldridge, M.E. / Satyshur, K.A. / Forest, K.T.
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 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6596
Polymers37,2081
Non-polymers1,4505
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.129, 55.072, 69.969
Angle α, β, γ (deg.)90.00, 92.23, 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: 37208.332 Da / Num. of mol.: 1
Fragment: monomeric chromophore binidng domain (UNP Residues 1-321)
Mutation: F145S, D207H, Y263F, L311E, L314E
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

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Non-polymers , 5 types, 321 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 3% v/v PEG 1000, 20% v/v ethanol, 6% v/v glycerol, 0.1M phosphate citrate, pH 4.2, 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: Mar 5, 2011 / 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
ReflectionRedundancy: 3.6 % / Number: 132344 / Rmerge(I) obs: 0.06 / Χ2: 1.06 / D res high: 1.76 Å / D res low: 30 Å / Num. obs: 36487 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.773098.710.0340.9213.5
3.794.7799.910.0391.133.6
3.313.7999.910.0521.413.6
3.013.3199.910.0541.4193.6
2.793.0199.910.0511.3183.6
2.632.7999.910.0591.3353.6
2.52.6399.910.071.2363.6
2.392.599.910.081.4333.6
2.32.3910010.0791.2833.6
2.222.310010.0821.2853.7
2.152.2210010.0831.1093.6
2.092.1510010.0881.0253.6
2.032.0910010.0930.9253.6
1.982.0310010.1080.933.6
1.941.9810010.120.8913.6
1.91.9410010.1350.8153.6
1.861.910010.1630.763.7
1.821.8610010.1750.6973.6
1.791.8210010.2040.6783.7
1.761.7910010.2250.6383.6
ReflectionResolution: 1.748→30 Å / Num. all: 36722 / Num. obs: 36431 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.06 / Net I/σ(I): 22.1
Reflection shellResolution: 1.748→1.79 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.225 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.45 Å
Translation2.5 Å28.45 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 1.748→27.65 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.572 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21693 1822 5 %RANDOM
Rwork0.18734 ---
obs0.18881 34609 99.18 %-
all-36431 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.1 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.748→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 103 316 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022563
X-RAY DIFFRACTIONr_bond_other_d0.0040.021727
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9993519
X-RAY DIFFRACTIONr_angle_other_deg0.9653.0024214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41723.119109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0361521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
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_it0.641.51583
X-RAY DIFFRACTIONr_mcbond_other0.0621.5627
X-RAY DIFFRACTIONr_mcangle_it1.19922559
X-RAY DIFFRACTIONr_scbond_it1.423978
X-RAY DIFFRACTIONr_scangle_it2.4164.5947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 113 -
Rwork0.199 2268 -
obs--91.79 %
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)
10.6631-0.4752-0.05840.4440.39331.2653-0.0818-0.0957-0.0217-0.02030.07040.0181-0.1996-0.00020.01140.1131-0.0243-0.0180.04560.00510.0328-9.190236.410521.4264
20.64750.39560.4450.43380.1350.42270.0816-0.10150.04860.0185-0.06050.08730.0483-0.0584-0.0210.0761-0.0301-0.00260.05390.00120.064-20.442320.754710.5859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 130
2X-RAY DIFFRACTION2A138 - 334

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