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- PDB-7sfa: Branchiostoma floridae fluorescent protein LanFP10A2 -

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Basic information

Entry
Database: PDB / ID: 7sfa
TitleBranchiostoma floridae fluorescent protein LanFP10A2
ComponentsFluorescent protein lanFP10A2
KeywordsFLUORESCENT PROTEIN / Gly-Tyr-Ala chromophore / chromophore
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPletnev, S. / Pletneva, N. / Pletnev, V.Z. / Muslinkina, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci. / Year: 2022
Title: A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins.
Authors: Roldan-Salgado, A. / Muslinkina, L. / Pletnev, S. / Pletneva, N. / Pletnev, V. / Gaytan, P.
History
DepositionOct 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein lanFP10A2
B: Fluorescent protein lanFP10A2
C: Fluorescent protein lanFP10A2
D: Fluorescent protein lanFP10A2


Theoretical massNumber of molelcules
Total (without water)107,3814
Polymers107,3814
Non-polymers00
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-33 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.238, 96.217, 158.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-465-

HOH

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Components

#1: Protein
Fluorescent protein lanFP10A2


Mass: 26845.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75522 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 24% PEG 2000 MME, 0.08 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 107864 / % possible obs: 98 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.035 / Rrim(I) all: 0.088 / Χ2: 0.859 / Net I/σ(I): 8 / Num. measured all: 624457
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.715.70.781104810.7270.3420.8560.8396.4
1.71-1.785.80.569104500.8320.2490.6230.83696.2
1.78-1.865.70.406105420.910.1780.4450.85396.4
1.86-1.965.70.26105610.9590.1140.2850.86896.9
1.96-2.085.60.174107040.9790.0770.1910.86698
2.08-2.245.50.124107770.9890.0550.1360.85298.4
2.24-2.465.50.092109210.9940.0410.1010.84699.1
2.46-2.825.60.079109400.9940.0350.0870.92999
2.82-3.555.90.068109990.9950.030.0740.92799
3.55-306.80.029114890.9990.0120.0310.899.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M9X

6m9x


Resolution: 1.65→27.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.841 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1096 1 %RANDOM
Rwork0.165 ---
obs0.1653 106693 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.51 Å2 / Biso mean: 17.962 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.31 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.65→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 0 660 7644
Biso mean---26.04 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0147364
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176407
X-RAY DIFFRACTIONr_angle_refined_deg1.881.6859996
X-RAY DIFFRACTIONr_angle_other_deg1.0541.64915094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.7575899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83523.408358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.893151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9251524
X-RAY DIFFRACTIONr_chiral_restr0.090.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028341
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021475
LS refinement shellResolution: 1.65→1.692 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.241 70 -
Rwork0.246 7681 -
obs--95.93 %

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