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- PDB-7swu: Crystal structure of the chromoprotein spisPINK -

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Basic information

Entry
Database: PDB / ID: 7swu
TitleCrystal structure of the chromoprotein spisPINK
ComponentsChromoprotein spisPINK
KeywordsFLUORESCENT PROTEIN / chromoprotein
Biological speciesStylophora pistillata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.444 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Oct 23, 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: Chromoprotein spisPINK
B: Chromoprotein spisPINK
C: Chromoprotein spisPINK
D: Chromoprotein spisPINK


Theoretical massNumber of molelcules
Total (without water)99,8354
Polymers99,8354
Non-polymers00
Water16,304905
1
A: Chromoprotein spisPINK
D: Chromoprotein spisPINK


Theoretical massNumber of molelcules
Total (without water)49,9182
Polymers49,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-4 kcal/mol
Surface area17540 Å2
MethodPISA
2
B: Chromoprotein spisPINK
C: Chromoprotein spisPINK


Theoretical massNumber of molelcules
Total (without water)49,9182
Polymers49,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-4 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.825, 83.742, 88.469
Angle α, β, γ (deg.)90, 96.81, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chromoprotein spisPINK


Mass: 24958.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stylophora pistillata (invertebrata) / Plasmid: pETcc2 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) polyethylene glycol 3350, 0.2 M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.444→87.844 Å / Num. obs: 157325 / % possible obs: 94.1 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.053 / Rrim(I) all: 0.14 / Net I/σ(I): 8.8
Reflection shellResolution: 1.444→1.536 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.606 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7867 / CC1/2: 0.523 / Rpim(I) all: 0.645 / Rrim(I) all: 1.732 / % possible all: 56.9

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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: 1.444→87.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 7850 -RANDOM
Rwork0.1754 ---
obs0.1763 157325 84.5 %-
Displacement parametersBiso mean: 20.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.4694 Å20 Å2-0.0058 Å2
2--0.1398 Å20 Å2
3----0.6092 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.444→87.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6826 0 0 905 7731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814266HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0725863HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4227SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2293HARMONIC5
X-RAY DIFFRACTIONt_it7262HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion923SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11579SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.42
X-RAY DIFFRACTIONt_other_torsion13.05
LS refinement shellResolution: 1.444→1.5 Å
RfactorNum. reflection% reflection
Rfree0.2956 180 -
Rwork0.2563 --
obs--15.17 %
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)
10.4341-0.05860.15190.42090.0750.2754-0.0022-0.0397-0.0082-0.0397-0.02480.0026-0.00820.00260.027-0.0103-0.00140.0021-0.02050.0093-0.01257.34310.115541.5371
20.4098-0.0836-0.13950.3521-0.10530.24910.0075-0.04140.0075-0.0414-0.02640.00550.00750.00550.0189-0.007-0.0015-0.007-0.0194-0.0101-0.009818.1051-17.925841.4457
30.4135-0.0367-0.04910.71690.06950.6515-0.01310.12510.07630.1251-0.0032-0.00380.0763-0.00380.01630.009-0.0097-0.0098-0.00310.0344-0.040812.0079-19.067772.1665
40.489-0.02520.17890.6249-0.11170.6472-0.02560.1309-0.0790.13090.0006-0.012-0.079-0.0120.0250.0152-0.00710.0045-0.0006-0.0318-0.047213.806711.075472.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 65
2X-RAY DIFFRACTION1{ A|* }A66
3X-RAY DIFFRACTION1{ A|* }A69 - 224
4X-RAY DIFFRACTION2{ B|* }B6 - 65
5X-RAY DIFFRACTION2{ B|* }B66
6X-RAY DIFFRACTION2{ B|* }B69 - 224
7X-RAY DIFFRACTION3{ C|* }C6 - 65
8X-RAY DIFFRACTION3{ C|* }C66
9X-RAY DIFFRACTION3{ C|* }C69 - 224
10X-RAY DIFFRACTION4{ D|* }D8 - 65
11X-RAY DIFFRACTION4{ D|* }D66
12X-RAY DIFFRACTION4{ D|* }D69 - 224

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