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- PDB-7z7q: Structure of the T207D single-point mutant of the fluorescent pro... -

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Basic information

Entry
Database: PDB / ID: 7z7q
TitleStructure of the T207D single-point mutant of the fluorescent protein NeonCyan1 at pH 6.5
ComponentsNeonCyan1
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: 1.6 Å
AuthorsDuarte, K. / 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 / 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 2.2Oct 16, 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: NeonCyan1
B: NeonCyan1
C: NeonCyan1
D: NeonCyan1


Theoretical massNumber of molelcules
Total (without water)106,6274
Polymers106,6274
Non-polymers00
Water6,215345
1
A: NeonCyan1


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NeonCyan1


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NeonCyan1


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NeonCyan1


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.063, 57.981, 71.446
Angle α, β, γ (deg.)68.570, 89.940, 89.580
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NeonCyan1 / Modified green fluorescent protein blFP-Y3


Mass: 26656.734 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.: 345 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM HEPES pH 6.5 and 22% PEG8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40.06 Å / Num. obs: 85638 / % possible obs: 86.7 % / Redundancy: 1.7 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.109 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8266 / CC1/2: 0.703 / Rrim(I) all: 0.754 / % possible all: 83.6

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Processing

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

5ltr


Resolution: 1.6→40.06 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.136 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 4327 5 %RANDOM
Rwork0.2232 ---
obs0.2248 81404 86.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.44 Å2 / Biso mean: 15.588 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.02 Å2-0.01 Å2
2--0 Å2-0.01 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6925 0 0 345 7270
Biso mean---20.91 -
Num. residues----869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137201
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156319
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.6899794
X-RAY DIFFRACTIONr_angle_other_deg1.3771.58714560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62723.436358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.838151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.321522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021724
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.522 303 -
Rwork0.458 5620 -
obs--81.23 %

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