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- PDB-8ag8: Structure of the Fluorescence Recovery-like protein FRPL from Pse... -

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Basic information

Entry
Database: PDB / ID: 8ag8
TitleStructure of the Fluorescence Recovery-like protein FRPL from Pseudomonas borbori
ComponentsFluorescence Recovery-like protein
KeywordsPROTEIN BINDING / Stress-related / Alpha-Helical bundle / Dimer
Function / homologyFluorescence recovery protein / : / Photoprotection regulator fluorescence recovery protein / thylakoid membrane / Fluorescence recovery protein (RFP)
Function and homology information
Biological speciesPseudomonas borbori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeiland, P. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Ecol Evol / Year: 2023
Title: Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection.
Authors: Steube, N. / Moldenhauer, M. / Weiland, P. / Saman, D. / Kilb, A. / Ramirez Rojas, A.A. / Garg, S.G. / Schindler, D. / Graumann, P.L. / Benesch, J.L.P. / Bange, G. / Friedrich, T. / Hochberg, G.K.A.
History
DepositionJul 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescence Recovery-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6112
Polymers13,4031
Non-polymers2071
Water1,29772
1
A: Fluorescence Recovery-like protein
hetero molecules

A: Fluorescence Recovery-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2214
Polymers26,8072
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2330 Å2
ΔGint-6 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.460, 53.460, 92.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Fluorescence Recovery-like protein / FRPL


Mass: 13403.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas borbori (bacteria) / Gene: SAMN05216190_11792 / Plasmid: pET-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I5SVP7
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.2 M LiSO4, 0.1 M CHES pH 9.5, and 1.4 M Sodium/Potassium Tartrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→46.334 Å / Num. obs: 13026 / % possible obs: 98.21 % / Redundancy: 22.2 % / CC1/2: 1 / Net I/σ(I): 32.02
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 1220 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZ0

5tz0


Resolution: 1.8→35 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 642 5 %
Rwork0.2274 --
obs0.2277 12831 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 13 72 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02907
X-RAY DIFFRACTIONf_angle_d1.4611219
X-RAY DIFFRACTIONf_dihedral_angle_d24.087128
X-RAY DIFFRACTIONf_chiral_restr0.108129
X-RAY DIFFRACTIONf_plane_restr0.01154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.41591190.31962255X-RAY DIFFRACTION93
1.94-2.130.28411280.24822421X-RAY DIFFRACTION99
2.13-2.440.30741260.23972411X-RAY DIFFRACTION98
2.44-3.080.24461300.24192465X-RAY DIFFRACTION100
3.08-350.19111390.20922637X-RAY DIFFRACTION100

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