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- PDB-6s67: Structure of the Fluorescent Protein AausFP1 from Aequorea cf. au... -

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Basic information

Entry
Database: PDB / ID: 6s67
TitleStructure of the Fluorescent Protein AausFP1 from Aequorea cf. australis at pH 7.0
ComponentsAequorea cf. australis fluorescent protein 1 (AausFP1)
KeywordsFLUORESCENT PROTEIN / GFP-like fluorescent protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein FP1
Function and homology information
Biological speciesAequorea australis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 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 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aequorea cf. australis fluorescent protein 1 (AausFP1)
B: Aequorea cf. australis fluorescent protein 1 (AausFP1)
C: Aequorea cf. australis fluorescent protein 1 (AausFP1)
D: Aequorea cf. australis fluorescent protein 1 (AausFP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4019
Polymers102,9414
Non-polymers4605
Water6,125340
1
A: Aequorea cf. australis fluorescent protein 1 (AausFP1)
B: Aequorea cf. australis fluorescent protein 1 (AausFP1)
hetero molecules


  • defined by author&software
  • Evidence: The analysis of the interaction interfaces has been performed with PISA. There are two dimers in the assymetric unit formed of monomers A and B on one hand, and of monomers C and D on the other hand.
  • 51.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)51,6554
Polymers51,4702
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-7 kcal/mol
Surface area17680 Å2
MethodPISA
2
C: Aequorea cf. australis fluorescent protein 1 (AausFP1)
D: Aequorea cf. australis fluorescent protein 1 (AausFP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7475
Polymers51,4702
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-7 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.080, 101.410, 161.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24B
15A
25C
16A
26D
17B
27C
18B
28D
19B
29C
110B
210D
111C
211D
112C
212D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVALAA7 - 647 - 64
21LEULEUVALVALBB7 - 647 - 64
12LEULEUVALVALAA7 - 647 - 64
22LEULEUVALVALCC7 - 647 - 64
13LEULEUVALVALAA7 - 647 - 64
23LEULEUVALVALDD7 - 647 - 64
14ALAALAALAALAAA68 - 23266 - 230
24ALAALAALAALABB68 - 23266 - 230
15ALAALAALAALAAA68 - 23266 - 230
25ALAALAALAALACC68 - 23266 - 230
16ALAALAALAALAAA68 - 23266 - 230
26ALAALAALAALADD68 - 23266 - 230
17LEULEUVALVALBB7 - 647 - 64
27LEULEUVALVALCC7 - 647 - 64
18LEULEUVALVALBB7 - 647 - 64
28LEULEUVALVALDD7 - 647 - 64
19ALAALAALAALABB68 - 23266 - 230
29ALAALAALAALACC68 - 23266 - 230
110ALAALAALAALABB68 - 23266 - 230
210ALAALAALAALADD68 - 23266 - 230
111LEULEUVALVALCC7 - 647 - 64
211LEULEUVALVALDD7 - 647 - 64
112ALAALAALAALACC68 - 23266 - 230
212ALAALAALAALADD68 - 23266 - 230

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Aequorea cf. australis fluorescent protein 1 (AausFP1)


Mass: 25735.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The CRO chromophore is formed upon autocatalytic cyclization of the three consecutive amino acid residues T, Y and G.
Source: (gene. exp.) Aequorea australis (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5J6CYI5*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.59 Å3/Da / Density % sol: 52.43 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.9 M trisodium citrate, 0.2 M sodium chloride, 0.1M Tris pH 7.0

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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: Feb 15, 2019 / Details: KB mirrors
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.47→48.42 Å / Num. obs: 39086 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.215 / Net I/σ(I): 9.72
Reflection shellResolution: 2.47→2.5 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 2845 / CC1/2: 0.707 / % possible all: 99.9

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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: 2.47→48.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.535 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.259
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2043 5.2 %RANDOM
Rwork0.1824 ---
obs0.1848 37043 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.9 Å2 / Biso mean: 34.892 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--5.09 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: final / Resolution: 2.47→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7068 0 1837 340 9245
Biso mean--41.92 32.68 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176780
X-RAY DIFFRACTIONr_angle_refined_deg1.661.66810052
X-RAY DIFFRACTIONr_angle_other_deg1.2141.5915822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5625924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8523.453362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.956151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.481529
X-RAY DIFFRACTIONr_chiral_restr0.0630.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021483
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A15210.09
12B15210.09
21A15330.08
22C15330.08
31A15360.08
32D15360.08
41A49930.07
42B49930.07
51A49600.07
52C49600.07
61A50100.06
62D50100.06
71B15180.11
72C15180.11
81B15580.08
82D15580.08
91B50260.07
92C50260.07
101B50370.08
102D50370.08
111C15430.1
112D15430.1
121C50710.07
122D50710.07
LS refinement shellResolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 151 -
Rwork0.295 2693 -
all-2844 -
obs--99.89 %

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