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- PDB-7swt: Crystal structure of the chromoprotein eforRED -

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Basic information

Entry
Database: PDB / ID: 7swt
TitleCrystal structure of the chromoprotein eforRED
ComponentsChromoprotein eforRED
KeywordsFLUORESCENT PROTEIN / chromoprotein
Biological speciesEchinopora forskaliana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsCaputo, A.T. / Newman, J. / 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromoprotein eforRED
B: Chromoprotein eforRED
C: Chromoprotein eforRED
D: Chromoprotein eforRED


Theoretical massNumber of molelcules
Total (without water)102,6984
Polymers102,6984
Non-polymers00
Water5,531307
1
A: Chromoprotein eforRED
C: Chromoprotein eforRED


Theoretical massNumber of molelcules
Total (without water)51,3492
Polymers51,3492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-15 kcal/mol
Surface area17880 Å2
MethodPISA
2
B: Chromoprotein eforRED
D: Chromoprotein eforRED


Theoretical massNumber of molelcules
Total (without water)51,3492
Polymers51,3492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-13 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.348, 75.859, 175.791
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromoprotein eforRED


Mass: 25674.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The fluorophore at position 63 is formed by the autocatalytic conversion of residues MYG
Source: (gene. exp.) Echinopora forskaliana (invertebrata) / Plasmid: pETcc2 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) polyethylene glycol 8000, 0.2 M sodium acetate, 0.1 M sodium MES (pH 6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.005→87.896 Å / Num. obs: 34510 / % possible obs: 87.5 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Net I/σ(I): 12.4
Reflection shellResolution: 2.005→2.222 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1725 / CC1/2: 0.718 / Rpim(I) all: 0.374 / Rrim(I) all: 1.355 / % possible all: 87.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SWR

7swr


Resolution: 2.005→87.89 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.705 / SU Rfree Blow DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1729 -RANDOM
Rwork0.209 ---
obs0.2111 34510 51.8 %-
Displacement parametersBiso mean: 36.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.2478 Å20 Å20 Å2
2--2.9781 Å20 Å2
3----5.2259 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.005→87.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 0 307 7398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914227HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1125763HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3990SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2327HARMONIC5
X-RAY DIFFRACTIONt_it7328HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion896SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact10120SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion17.11
LS refinement shellResolution: 2.005→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3108 37 -
Rwork0.2785 --
obs--6.23 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84220.17530.28290.83020.22782.8383-0.01980.02820.22360.02820.05110.38570.22360.3857-0.0313-0.04040.06880.00690.0266-0.0654-0.101110.500420.750417.7486
20.7761-0.1228-0.21520.86180.5712.70510.0097-0.1977-0.7992-0.1977-0.0227-0.0657-0.7992-0.06570.01290.25260.0161-0.0132-0.10450.0148-0.12991.096350.430319.1461
30.8255-0.4459-0.11651.01160.59572.3963-0.04220.19820.63790.1982-0.1928-0.64560.6379-0.64560.2350.0646-0.22230.08190.093-0.1139-0.0854-17.790811.495227.259
40.61480.41060.24081.28940.57593.1394-0.02130.0401-0.42240.0401-0.2759-1.0827-0.4224-1.08270.2972-0.0690.25690.01020.358-0.1621-0.1036-25.78141.111332.1671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 61
2X-RAY DIFFRACTION1{ A|* }A62
3X-RAY DIFFRACTION1{ A|* }A65 - 225
4X-RAY DIFFRACTION2{ B|* }B3 - 61
5X-RAY DIFFRACTION2{ B|* }B62
6X-RAY DIFFRACTION2{ B|* }B65 - 224
7X-RAY DIFFRACTION3{ C|* }C3 - 61
8X-RAY DIFFRACTION3{ C|* }C62
9X-RAY DIFFRACTION3{ C|* }C65 - 224
10X-RAY DIFFRACTION4{ D|* }D3 - 61
11X-RAY DIFFRACTION4{ D|* }D62
12X-RAY DIFFRACTION4{ D|* }D65 - 224

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