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- PDB-7z7o: Structure of the fluorescent protein NeonCyan0.95 at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 7z7o
TitleStructure of the fluorescent protein NeonCyan0.95 at pH 7.5
ComponentsNeonCyan0.95
KeywordsFLUORESCENT PROTEIN / mNeonGreen / Trp-based fluorescent chromophore / rational design
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Green fluorescent protein blFP-Y3
Function and homology information
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsClavel, D. / Dupuy, J. / Royant, A.
Funding support France, United States, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0013 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM109984 United States
CitationJournal: Protein Eng.Des.Sel. / Year: 2022
Title: Cyan fluorescent proteins derived from mNeonGreen.
Authors: Zarowny, L. / Clavel, D. / Johannson, R. / Duarte, K. / Depernet, H. / Dupuy, J. / Baker, H. / Brown, A. / Royant, A. / Campbell, R.E.
History
DepositionMar 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
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 / pdbx_validate_main_chain_plane / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 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: NeonCyan0.95
B: NeonCyan0.95
C: NeonCyan0.95
D: NeonCyan0.95


Theoretical massNumber of molelcules
Total (without water)106,4434
Polymers106,4434
Non-polymers00
Water8,827490
1
A: NeonCyan0.95
C: NeonCyan0.95


Theoretical massNumber of molelcules
Total (without water)53,2212
Polymers53,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-10 kcal/mol
Surface area18170 Å2
MethodPISA
2
B: NeonCyan0.95

D: NeonCyan0.95


Theoretical massNumber of molelcules
Total (without water)53,2212
Polymers53,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.852, 60.662, 67.074
Angle α, β, γ (deg.)89.950, 71.790, 90.010
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NeonCyan0.95 / Modified green fluorescent protein blFP-Y3


Mass: 26610.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residue CRC69 is formed by the autocatalytic cyclisation of the consecutive amino acid residues GWG, hence the mismatch in the sequence alignment
Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-Y3 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PNC0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 1.6 Å3/Da / Density % sol: 23.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES pH 7.5 and 18% w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2017
RadiationMonochromator: Laue [110] diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.51→63.71 Å / Num. obs: 127042 / % possible obs: 84.7 % / Redundancy: 1.6 % / CC1/2: 0.999 / Rrim(I) all: 0.046 / Net I/σ(I): 6.4
Reflection shellResolution: 1.51→1.64 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6974 / CC1/2: 0.84 / Rrim(I) all: 0.577 / % possible all: 51.4

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTR

5ltr


Resolution: 1.51→63.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.305 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 3938 3.4 %RANDOM
Rwork0.1634 ---
obs0.1644 112268 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.77 Å2 / Biso mean: 28.608 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.01 Å2
2--0 Å20.01 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.51→63.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 0 490 7582
Biso mean---36.86 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156481
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6899960
X-RAY DIFFRACTIONr_angle_other_deg1.3361.58614915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85423.25360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0551524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021752
LS refinement shellResolution: 1.514→1.554 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 19 -
Rwork0.232 8599 -
all-8618 -
obs--100 %

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