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- PDB-8ths: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -

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Basic information

Entry
Database: PDB / ID: 8ths
TitleCrystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA A69T
ComponentsKAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T
KeywordsFLUORESCENT PROTEIN / BETA BARREL / LUMINESCENT PROTEIN
Function / homologyNITRATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHenderson, J.N. / Mills, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1817947 United States
CitationJournal: Front Chem / Year: 2023
Title: Capturing excited-state structural snapshots of evolutionary green-to-red photochromic fluorescent proteins.
Authors: Krueger, T.D. / Henderson, J.N. / Breen, I.L. / Zhu, L. / Wachter, R.M. / Mills, J.H. / Fang, C.
History
DepositionJul 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: 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 / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Oct 9, 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: KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T
B: KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T
C: KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T
D: KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,59113
Polymers105,8564
Non-polymers7359
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint1 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.447, 106.084, 123.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T


Mass: 26464.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 microliters of protein at 20 mg/mL in 10 mM HEPES pH 7.5 + 75 mM NaCl mixed with 2 microliters of well solution containing 35% PEG 3350 + 0.3 M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→48.74 Å / Num. obs: 152026 / % possible obs: 99.8 % / Redundancy: 7.8 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Χ2: 0.99 / Net I/σ(I): 18.3 / Num. measured all: 1183642
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 97.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.814 / Num. measured all: 33660 / Num. unique obs: 7274 / CC1/2: 0.331 / Rpim(I) all: 0.927 / Rrim(I) all: 2.05 / Χ2: 0.95 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.03 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.165 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18806 7617 5 %RANDOM
Rwork0.16232 ---
obs0.1636 144318 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6973 0 48 962 7983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156696
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.65910049
X-RAY DIFFRACTIONr_angle_other_deg1.4821.58215517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7835921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9322.577388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.773151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3481532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021701
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.5363555
X-RAY DIFFRACTIONr_mcbond_other0.9711.5363554
X-RAY DIFFRACTIONr_mcangle_it1.4872.3024449
X-RAY DIFFRACTIONr_mcangle_other1.4872.3034450
X-RAY DIFFRACTIONr_scbond_it1.581.6993855
X-RAY DIFFRACTIONr_scbond_other1.5761.6973853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3492.475571
X-RAY DIFFRACTIONr_long_range_B_refined5.23519.7078178
X-RAY DIFFRACTIONr_long_range_B_other4.97418.3747864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 530 -
Rwork0.326 10388 -
obs--97.56 %
Refinement TLS params.

Method: refined / 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)
11.2173-0.33860.28421.17450.12280.8280.05570.0796-0.0488-0.1582-0.09940.1259-0.0036-0.05310.04360.0470.01-0.01540.0159-0.01240.023427.333.067.554
20.89530.0089-0.00941.33570.25550.7711-0.0225-0.12270.01610.069-0.06360.16490.0395-0.08440.0860.0051-0.00280.01010.0273-0.01550.024824.7320.97133.335
31.25320.3536-0.08461.30520.24941.17730.0352-0.12030.07250.07430.013-0.1376-0.05520.0862-0.04830.0151-0.0076-0.01840.0185-0.00860.048455.26921.79635.594
40.98740.1612-0.12190.82950.13170.9387-0.03830.0972-0.104-0.09250.0831-0.1607-0.02590.1022-0.04480.0388-0.00970.04870.0282-0.020.073457.288.57.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 221
2X-RAY DIFFRACTION2B4 - 222
3X-RAY DIFFRACTION3C4 - 220
4X-RAY DIFFRACTION4D4 - 222

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