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- PDB-5tz0: Structure of the Fremyella diplosiphon Fluorescence Recovery Protein -

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Basic information

Entry
Database: PDB / ID: 5tz0
TitleStructure of the Fremyella diplosiphon Fluorescence Recovery Protein
ComponentsFluorescence Recovery Protein
KeywordsPROTEIN BINDING / PHOTOPROTECTION / NON-PHOTOCHEMICAL QUENCHING
Function / homologyFluorescence recovery protein / : / Photoprotection regulator fluorescence recovery protein / thylakoid membrane / Fluorescence recovery protein
Function and homology information
Biological speciesTolypothrix sp. PCC 7601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.025 Å
AuthorsSutter, M. / Pawlowski, E.G. / Kerfeld, C.A.
CitationJournal: Nat Plants / Year: 2017
Title: Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria.
Authors: Bao, H. / Melnicki, M.R. / Pawlowski, E.G. / Sutter, M. / Agostoni, M. / Lechno-Yossef, S. / Cai, F. / Montgomery, B.L. / Kerfeld, C.A.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescence Recovery Protein
B: Fluorescence Recovery Protein


Theoretical massNumber of molelcules
Total (without water)27,0602
Polymers27,0602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-14 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.628, 77.506, 31.968
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fluorescence Recovery Protein


Mass: 13530.222 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. PCC 7601 (bacteria) / Gene: FDUTEX481_08603 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6KMZ1

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 14% PEG-3000 0.1 M tri-sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→38.753 Å / Num. obs: 5519 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.7
Reflection shellResolution: 3.02→3.19 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.754 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDX

4jdx


Resolution: 3.025→38.753 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.49
RfactorNum. reflection% reflection
Rfree0.2922 556 10.11 %
Rwork0.2405 --
obs0.2457 5501 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.025→38.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 0 0 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031725
X-RAY DIFFRACTIONf_angle_d0.572328
X-RAY DIFFRACTIONf_dihedral_angle_d13.8191026
X-RAY DIFFRACTIONf_chiral_restr0.034254
X-RAY DIFFRACTIONf_plane_restr0.003297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0248-3.32910.40871430.33081201X-RAY DIFFRACTION99
3.3291-3.81040.33741350.27641241X-RAY DIFFRACTION100
3.8104-4.79930.2721350.2161249X-RAY DIFFRACTION100
4.7993-38.75620.24921430.21331254X-RAY DIFFRACTION100

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