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- PDB-7swr: Crystal structure of the chromoprotein gfasPurple -

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Basic information

Entry
Database: PDB / ID: 7swr
TitleCrystal structure of the chromoprotein gfasPurple
ComponentsChromoprotein gfasPurple
KeywordsFLUORESCENT PROTEIN / chromoprotein
Biological speciesGalaxea fascicularis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.388 Å
AuthorsCaputo, A.T. / Newman, J. / Peat, T.S. / Scott, C. / Ahmed, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Over the rainbow: structural characterization of the chromoproteins gfasPurple, amilCP, spisPink and eforRed.
Authors: Ahmed, F.H. / Caputo, A.T. / French, N.G. / Peat, T.S. / Whitfield, J. / Warden, A.C. / Newman, J. / Scott, C.
History
DepositionNov 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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
Revision 2.1Nov 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:
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Assembly

Deposited unit
A: Chromoprotein gfasPurple
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9304
Polymers24,8241
Non-polymers1063
Water7,098394
1
A: Chromoprotein gfasPurple
hetero molecules

A: Chromoprotein gfasPurple
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8618
Polymers49,6482
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2780 Å2
ΔGint-63 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.136, 92.136, 78.52
Angle α, β, γ (deg.)90, 90, 90
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

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Components

#1: Protein Chromoprotein gfasPurple


Mass: 24824.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 62-64 QYG undergo autocatalytic modifcation to chromophore modelled as residue CRQ
Source: (gene. exp.) Galaxea fascicularis (invertebrata) / Plasmid: pETcc2 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v polyethylene glycol 3350, 0.2 M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.388→92.136 Å / Num. obs: 56552 / % possible obs: 96.1 % / Redundancy: 46.4 % / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.026 / Rrim(I) all: 0.126 / Net I/σ(I): 21.6
Reflection shellResolution: 1.388→1.467 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2826 / CC1/2: 0.708 / Rpim(I) all: 0.582 / Rrim(I) all: 2.249 / % possible all: 71.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IR8

3ir8


Resolution: 1.388→19.93 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.968 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.1726 2886 -RANDOM
Rwork0.1621 ---
obs0.1627 56516 82.4 %-
Displacement parametersBiso mean: 19.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.2354 Å20 Å20 Å2
2---0.2354 Å20 Å2
3---0.4709 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.388→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 3 394 2131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083680HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.086673HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1081SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes584HARMONIC5
X-RAY DIFFRACTIONt_it1887HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3154SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.69
X-RAY DIFFRACTIONt_other_torsion15.59
LS refinement shellResolution: 1.39→1.43 Å
RfactorNum. reflection% reflection
Rfree0.2593 51 -
Rwork0.2446 --
obs0.2452 1131 18.11 %
Refinement TLS params.Origin x: -29.7428 Å / Origin y: -0.6109 Å / Origin z: -15.7028 Å
111213212223313233
T-0.0223 Å2-0.0131 Å20.0096 Å2--0.0129 Å2-0.0044 Å2--0.0007 Å2
L0.5668 °2-0.0492 °2-0.0881 °2-0.165 °20.0562 °2--0.2614 °2
S-0.017 Å °-0.0323 Å °0.0189 Å °-0.0323 Å °0.0322 Å °0.0397 Å °0.0189 Å °0.0397 Å °-0.0151 Å °
Refinement TLS groupSelection details: { A|* }

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