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- PDB-4jdq: Structure of the Fluorescence Recovery Protein from Synechocystis... -

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Basic information

Entry
Database: PDB / ID: 4jdq
TitleStructure of the Fluorescence Recovery Protein from Synechocystis sp PCC 6803, R60K mutant
ComponentsSlr1964 protein
KeywordsPROTEIN BINDING / photoprotection / non-photochemical quenching
Function / homologyFluorescence recovery protein / : / Photoprotection regulator fluorescence recovery protein / plasma membrane-derived thylakoid membrane / Fluorescence recovery protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsSutter, M. / Kerfeld, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria.
Authors: Sutter, M. / Wilson, A. / Leverenz, R.L. / Lopez-Igual, R. / Thurotte, A. / Salmeen, A.E. / Kirilovsky, D. / Kerfeld, C.A.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Slr1964 protein
B: Slr1964 protein
C: Slr1964 protein
D: Slr1964 protein
E: Slr1964 protein
F: Slr1964 protein


Theoretical massNumber of molelcules
Total (without water)79,1226
Polymers79,1226
Non-polymers00
Water00
1
A: Slr1964 protein

C: Slr1964 protein


Theoretical massNumber of molelcules
Total (without water)26,3742
Polymers26,3742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x+1/2,-y-1/2,-z+3/41
Buried area1600 Å2
ΔGint-17 kcal/mol
Surface area11850 Å2
MethodPISA
2
B: Slr1964 protein
D: Slr1964 protein


Theoretical massNumber of molelcules
Total (without water)26,3742
Polymers26,3742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-18 kcal/mol
Surface area12200 Å2
MethodPISA
3
E: Slr1964 protein
F: Slr1964 protein

E: Slr1964 protein
F: Slr1964 protein


Theoretical massNumber of molelcules
Total (without water)52,7484
Polymers52,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10290 Å2
ΔGint-77 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.406, 87.406, 229.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Slr1964 protein


Mass: 13186.942 Da / Num. of mol.: 6 / Mutation: R60K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1964 / Production host: Escherichia coli (E. coli) / References: UniProt: P74103

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5% PEG-3350, 100mM Na-citrate, 2% tacsimate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 3.51→39.09 Å / Num. all: 11816 / Num. obs: 11769 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.51→3.7 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.01539 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1625 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→39.089 Å / SU ML: 0.49 / σ(F): 1.33 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 2076 9.94 %random
Rwork0.2334 ---
obs0.2372 11769 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.52→39.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 0 0 4673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044746
X-RAY DIFFRACTIONf_angle_d0.6956393
X-RAY DIFFRACTIONf_dihedral_angle_d14.6231741
X-RAY DIFFRACTIONf_chiral_restr0.046732
X-RAY DIFFRACTIONf_plane_restr0.002811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.60450.37361310.38531169X-RAY DIFFRACTION93
3.6045-3.69460.32971340.31011254X-RAY DIFFRACTION100
3.6946-3.79440.30921400.30441285X-RAY DIFFRACTION100
3.7944-3.9060.31441350.29061253X-RAY DIFFRACTION100
3.906-4.03190.34011430.25831248X-RAY DIFFRACTION100
4.0319-4.17590.34351390.24961280X-RAY DIFFRACTION100
4.1759-4.34290.28991410.26091252X-RAY DIFFRACTION100
4.3429-4.54020.2821430.2451253X-RAY DIFFRACTION100
4.5402-4.77920.27591480.20511253X-RAY DIFFRACTION100
4.7792-5.07810.23461400.2131253X-RAY DIFFRACTION100
5.0781-5.46920.23541380.21681266X-RAY DIFFRACTION100
5.4692-6.01780.32071400.22741257X-RAY DIFFRACTION100
6.0178-6.88450.34251390.24391265X-RAY DIFFRACTION100
6.8845-8.65810.22211350.19541262X-RAY DIFFRACTION100
8.6581-39.09150.22081300.20031267X-RAY DIFFRACTION100

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