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- PDB-4cqh: Structure of Infrared Fluorescent Protein IFP2.0 -

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Basic information

Entry
Database: PDB / ID: 4cqh
TitleStructure of Infrared Fluorescent Protein IFP2.0
ComponentsBACTERIOPHYTOCHROME
KeywordsFLUORESCENT PROTEIN / INFRARED FLUORESCENT 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 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: 1.14 Å
AuthorsLafaye, C. / Yu, D. / Noirclerc-Savoye, M. / Shu, X. / Royant, A.
Citation
Journal: Nat.Commun. / Year: 2014
Title: An Improved Monomeric Infrared Fluorescent Protein for Neuronal and Tumour Brain Imaging.
Authors: Yu, D. / Gustafson, W.C. / Han, C. / Lafaye, C. / Noirclerc-Savoye, M. / Ge, W. / Thayer, D.A. / Huang, H. / Kornberg, T.B. / Royant, A. / Jan, L.Y. / Jan, Y.N. / Weiss, W.A. / Shu, X.
#1: Journal: Science / Year: 2009
Title: Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome.
Authors: Shu, X. / Royant, A. / Lin, M.Z. / Aguilera, T.A. / Lev-Ram, V. / Steinbach, P.A. / Tsien, R.Y.
History
DepositionFeb 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 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: BACTERIOPHYTOCHROME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6013
Polymers35,9921
Non-polymers6092
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.692, 52.912, 66.316
Angle α, β, γ (deg.)90.00, 91.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein BACTERIOPHYTOCHROME / PHYTOCHROME-LIKE PROTEIN / INFRARED FLUORESCENT PROTEIN VERSION 2.0


Mass: 35991.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-317 / 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) / Variant (production host): RIL / References: UniProt: Q9RZA4
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIFP2.0 HAS BEEN ENGINEERED FROM A FRAGMENT OF THE BACTERIOPHYTOCHROME FROM DEINOCOCCUS RADIODURANS

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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: 2.27 Å3/Da / Density % sol: 45.78 % / Description: NONE
Crystal growpH: 4.6 / Details: 30% PEG 400, 100 MM SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2013 / Details: KB MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.14→46.3 Å / Num. obs: 114179 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 1.14→27.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.892 / SU ML: 0.019 / 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. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15996 6054 5 %RANDOM
Rwork0.1371 ---
obs0.13825 114179 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0.26 Å2
2---0.09 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.14→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 44 291 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192635
X-RAY DIFFRACTIONr_bond_other_d0.0010.022588
X-RAY DIFFRACTIONr_angle_refined_deg1.9632.0023653
X-RAY DIFFRACTIONr_angle_other_deg0.9535958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71622.617107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0541524
X-RAY DIFFRACTIONr_chiral_restr0.1360.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02606
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_it1.7511.1891296
X-RAY DIFFRACTIONr_mcbond_other1.7331.1861295
X-RAY DIFFRACTIONr_mcangle_it2.2921.7961636
X-RAY DIFFRACTIONr_mcangle_other2.3071.7991637
X-RAY DIFFRACTIONr_scbond_it2.5911.4361339
X-RAY DIFFRACTIONr_scbond_other2.591.4361340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1132.0741993
X-RAY DIFFRACTIONr_long_range_B_refined4.27511.3333132
X-RAY DIFFRACTIONr_long_range_B_other3.63210.5732961
X-RAY DIFFRACTIONr_rigid_bond_restr3.14435223
X-RAY DIFFRACTIONr_sphericity_free26.425569
X-RAY DIFFRACTIONr_sphericity_bonded9.86355354
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 481 -
Rwork0.221 8310 -
obs--99.65 %

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