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- PDB-6s68: Structure of the Fluorescent Protein AausFP2 from Aequorea cf. au... -

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Basic information

Entry
Database: PDB / ID: 6s68
TitleStructure of the Fluorescent Protein AausFP2 from Aequorea cf. australis at pH 7.6
ComponentsAequorea cf. australis fluorescent protein 2 (AausFP2)
KeywordsFLUORESCENT PROTEIN / GFP-like fluorescent protein
Biological speciesAequorea australis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsDepernet, H. / Gotthard, G. / Lambert, G.G. / Shaner, N.C. / Royant, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM109984-01 United States
CitationJournal: Plos Biol. / Year: 2020
Title: Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing.
Authors: Lambert, G.G. / Depernet, H. / Gotthard, G. / Schultz, D.T. / Navizet, I. / Lambert, T. / Adams, S.R. / Torreblanca-Zanca, A. / Chu, M. / Bindels, D.S. / Levesque, V. / Nero Moffatt, J. / ...Authors: Lambert, G.G. / Depernet, H. / Gotthard, G. / Schultz, D.T. / Navizet, I. / Lambert, T. / Adams, S.R. / Torreblanca-Zanca, A. / Chu, M. / Bindels, D.S. / Levesque, V. / Nero Moffatt, J. / Salih, A. / Royant, A. / Shaner, N.C.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity_poly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_poly.pdbx_strand_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 2.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aequorea cf. australis fluorescent protein 2 (AausFP2)


Theoretical massNumber of molelcules
Total (without water)25,5711
Polymers25,5711
Non-polymers00
Water2,666148
1
A: Aequorea cf. australis fluorescent protein 2 (AausFP2)

A: Aequorea cf. australis fluorescent protein 2 (AausFP2)


Theoretical massNumber of molelcules
Total (without water)51,1422
Polymers51,1422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3750 Å2
ΔGint-14 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 75.130, 100.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

21A-426-

HOH

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Components

#1: Protein Aequorea cf. australis fluorescent protein 2 (AausFP2)


Mass: 25571.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The PIA chromophore is formed upon autocatalytic cyclization of the three consecutive amino acid residues A, Y and G.
Source: (gene. exp.) Aequorea australis (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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 Å3/Da / Density % sol: 38.65 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 24% PEG 3350, 0.2 M sodium chloride, 0.1M HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2018 / Details: CRL Transfocator, Elliptical mirror
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.06→44.11 Å / Num. obs: 13079 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.1 / Net I/σ(I): 12.79
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 976 / CC1/2: 0.683 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: phiYFPv (Phialidium, PDB:4HE4)

4he4


Resolution: 2.06→44.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 9.351 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.167
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 632 4.8 %RANDOM
Rwork0.1665 ---
obs0.1683 12447 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.15 Å2 / Biso mean: 34.468 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å20 Å2
2--1.11 Å20 Å2
3---2.42 Å2
Refinement stepCycle: final / Resolution: 2.06→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 20 148 1905
Biso mean--28.93 44.21 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131831
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171675
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6582481
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5893901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0155233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33723.22693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.307159
X-RAY DIFFRACTIONr_chiral_restr0.0610.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
LS refinement shellResolution: 2.06→2.113 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 41 -
Rwork0.238 930 -
all-971 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: 17.716 Å / Origin y: 8.858 Å / Origin z: 13.574 Å
111213212223313233
T0.226 Å2-0.0203 Å2-0.0133 Å2-0.0337 Å20.0206 Å2--0.0168 Å2
L1.0276 °20.4176 °20.3565 °2-1.679 °2-0.7929 °2--2.223 °2
S-0.0967 Å °0.0356 Å °0.0504 Å °-0.198 Å °0.1917 Å °0.1651 Å °0.0106 Å °-0.2303 Å °-0.095 Å °

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