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- PDB-6y1g: Photoconverted HcRed in its optoacoustic state -

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Basic information

Entry
Database: PDB / ID: 6y1g
TitlePhotoconverted HcRed in its optoacoustic state
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsFLUORESCENT PROTEIN / reversible switchable fluorescent protein
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / GFP-like non-fluorescent chromoprotein
Function and homology information
Biological speciesHeteractis crispa (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJanowski, R. / Fuenzalida-Werner, J.P. / Mishra, K. / Stiel, A.C. / Niessing, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG SFB 1054 (TP B09) Germany
CitationJournal: Anal.Chem. / Year: 2020
Title: Challenging a Preconception: Optoacoustic Spectrum Differs from the Optical Absorption Spectrum of Proteins and Dyes for Molecular Imaging.
Authors: Fuenzalida Werner, J.P. / Huang, Y. / Mishra, K. / Janowski, R. / Vetschera, P. / Heichler, C. / Chmyrov, A. / Neufert, C. / Niessing, D. / Ntziachristos, V. / Stiel, A.C.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
B: GFP-like non-fluorescent chromoprotein
C: GFP-like non-fluorescent chromoprotein
D: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,91723
Polymers107,7384
Non-polymers1,17919
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint5 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.710, 75.200, 254.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GFP-like non-fluorescent chromoprotein / HcRed / hcCP


Mass: 26934.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heteractis crispa (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q95W85
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BICINE pH 8.5, 22% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 44173 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3184 / CC1/2: 0.673 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZW

1yzw


Resolution: 2.3→49.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.863 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.25
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 2181 4.9 %RANDOM
Rwork0.1679 ---
obs0.1717 41992 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.29 Å2 / Biso mean: 29.206 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.71 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 2.3→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 76 596 7780
Biso mean--57.8 34.89 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137428
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176738
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.689995
X-RAY DIFFRACTIONr_angle_other_deg1.3161.58715657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5725900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85721.584385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.263151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2021548
X-RAY DIFFRACTIONr_chiral_restr0.0810.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028268
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021644
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 143 -
Rwork0.259 3036 -
all-3179 -
obs--99.34 %
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)
10.41820.2323-0.01680.451-0.02630.55580.02960.0540.0208-0.00840.0066-0.04930.0883-0.0338-0.03620.0183-0.00610.00150.1996-0.03240.024410.1654-18.6352-45.6353
20.23240.0798-0.09180.2268-0.10960.37910.02160.0004-0.00210.01890.00980.03410.0310.012-0.03130.03940.0025-0.00880.16040.01250.01014.3807-16.5945-15.7076
30.2384-0.03690.06160.4951-0.00690.42130.03510.0145-0.01720.08250.0168-0.0172-0.0581-0.0312-0.05190.06750.01860.00350.1292-0.0160.010511.621613.0819-16.4533
40.50370.20010.07340.34820.0670.64740.02860.08220.0182-0.0129-0.00480.0257-0.05020.0444-0.02370.01220.01290.00310.19430.0310.009311.539211.9128-47.0403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 227
2X-RAY DIFFRACTION2B4 - 227
3X-RAY DIFFRACTION3C4 - 227
4X-RAY DIFFRACTION4D4 - 227

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