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- PDB-5ajg: Structure of Infrared Fluorescent Protein IFP1.4 AT 1.11 Angstrom... -

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Basic information

Entry
Database: PDB / ID: 5ajg
TitleStructure of Infrared Fluorescent Protein IFP1.4 AT 1.11 Angstrom resolution
ComponentsBACTERIOPHYTOCHROME
KeywordsFLUORESCENT PROTEIN
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 / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain ...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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / Bacteriophytochrome
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsLafaye, C. / Shu, X. / Royant, A.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.
Authors: Feliks, M. / Lafaye, C. / Shu, X. / Royant, A. / Field, M.
History
DepositionFeb 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Structure summary
Revision 1.3Aug 24, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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)36,5432
Polymers35,9571
Non-polymers5861
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.361, 53.028, 66.219
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

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Components

#1: Protein BACTERIOPHYTOCHROME / INFRARED FLUORESCENT PROTEIN IFP1.4 / PHYTOCHROME-LIKE PROTEIN


Mass: 35957.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Plasmid: PBAD / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.26 Å3/Da / Density % sol: 45.65 % / Description: NONE
Crystal growpH: 5 / Details: 26% PEG 400, 0.1 M SODIUM ACETATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.11→38.4 Å / Num. obs: 121711 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 14.239 Å2 / Rsym value: 0.03 / Net I/σ(I): 17.6
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.62 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CQH

4cqh


Resolution: 1.11→38.43 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.803 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COVALENT BOND BETWEEN ATOM SG OF CYS A24 AND ATOM CBA1 OF CHROMOPHORE LBV B1
RfactorNum. reflection% reflectionSelection details
Rfree0.16806 6417 5 %RANDOM
Rwork0.14581 ---
obs0.14693 121711 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.135 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.04 Å2
2--0.13 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.11→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 43 262 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192667
X-RAY DIFFRACTIONr_bond_other_d0.0020.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.9442.0043701
X-RAY DIFFRACTIONr_angle_other_deg0.9536052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35322.5112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85915434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1391526
X-RAY DIFFRACTIONr_chiral_restr0.1430.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213091
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
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_it2.2891.521296
X-RAY DIFFRACTIONr_mcbond_other2.2541.5171295
X-RAY DIFFRACTIONr_mcangle_it2.892.2851640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6561.7491371
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.27535291
X-RAY DIFFRACTIONr_sphericity_free23.68567
X-RAY DIFFRACTIONr_sphericity_bonded10.36755388
LS refinement shellResolution: 1.11→1.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 437 -
Rwork0.227 8467 -
obs--93.07 %

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