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- PDB-8afk: Structure of iRFP variant C15S/N136R/V256C in complex with phycoc... -

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Basic information

Entry
Database: PDB / ID: 8afk
TitleStructure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin
ComponentsNear-infrared fluorescent protein
KeywordsFLUORESCENT PROTEIN / iRFP / phytochrome / phycocyanobilin
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
PAS fold-2 / PAS fold / 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 domain superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Near-infrared fluorescent protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.015 Å
AuthorsRemeeva, A. / Kovalev, K. / Gushchin, I. / Fonin, A. / Turoverov, K. / Stepanenko, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin
Authors: Remeeva, A. / Kovalev, K. / Gushchin, I. / Fonin, A. / Turoverov, K. / Stepanenko, O.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Near-infrared fluorescent protein
B: Near-infrared fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5214
Polymers69,3432
Non-polymers1,1772
Water2,414134
1
A: Near-infrared fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2602
Polymers34,6721
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Near-infrared fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2602
Polymers34,6721
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.806, 98.708, 156.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Near-infrared fluorescent protein


Mass: 34671.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: iRFP / Production host: Escherichia coli (E. coli) / References: UniProt: G1FNL7
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG1000 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.015→69.7 Å / Num. obs: 30361 / % possible obs: 75.4 % / Redundancy: 13.6 % / CC1/2: 0.9994 / Rpim(I) all: 0.03 / Net I/σ(I): 14.257
Reflection shellResolution: 2.015→2.182 Å / Num. unique obs: 1898 / CC1/2: 0.2832 / Rpim(I) all: 1.406

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40000 / Resolution: 2.015→19.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1533 5.06 %RANDOM
Rwork0.2401 ---
obs0.2422 30312 75.4 %-
Displacement parametersBiso max: 101.18 Å2 / Biso mean: 57.27 Å2 / Biso min: 30.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.2082 Å20 Å20 Å2
2--1.2931 Å20 Å2
3----0.0849 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.015→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 86 134 4467
Biso mean--57.66 55.05 -
Num. residues----565
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1484SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes759HARMONIC5
X-RAY DIFFRACTIONt_it4483HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion607SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3611SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4483HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6118HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion19.21
LS refinement shellResolution: 2.02→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3981 22 3.62 %
Rwork0.3465 585 -
all0.3483 607 -
obs--10.85 %

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