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- PDB-6qq9: Cryogenic temperature structure of the fluorescent protein Cerule... -

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Basic information

Entry
Database: PDB / ID: 6qq9
TitleCryogenic temperature structure of the fluorescent protein Cerulean recorded after an accumulated dose of 5.8 MGy
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / tryptophan-based chromophore / Cerulean / hydrogen atoms
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / CARBON DIOXIDE / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å
AuthorsGotthard, G. / Aumonier, S. / Royant, A.
CitationJournal: Iucrj / Year: 2019
Title: Specific radiation damage is a lesser concern at room temperature.
Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A.
History
DepositionFeb 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8332
Polymers26,7891
Non-polymers441
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.410, 63.000, 70.530
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 Green fluorescent protein /


Mass: 26789.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES 7.0, 12% PEG8000, 100mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.82→46.99 Å / Num. obs: 21133 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.708 Å2 / CC1/2: 1 / Net I/σ(I): 28.23
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1544 / CC1/2: 0.726 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.82→46.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.202 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19519 1059 5 %RANDOM
Rwork0.15214 ---
obs0.15432 20075 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å2-0 Å2
2---1.13 Å20 Å2
3---1.92 Å2
Refinement stepCycle: 1 / Resolution: 1.82→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 3 228 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191957
X-RAY DIFFRACTIONr_bond_other_d0.0010.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9832688
X-RAY DIFFRACTIONr_angle_other_deg0.7033.0014150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6825.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.093156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_it1.9473.281958
X-RAY DIFFRACTIONr_mcbond_other1.9473.284959
X-RAY DIFFRACTIONr_mcangle_it2.8994.9041205
X-RAY DIFFRACTIONr_mcangle_other2.884.9031205
X-RAY DIFFRACTIONr_scbond_it2.4883.482999
X-RAY DIFFRACTIONr_scbond_other2.4733.481998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8915.1161465
X-RAY DIFFRACTIONr_long_range_B_refined7.13439.2632121
X-RAY DIFFRACTIONr_long_range_B_other7.05138.4482073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 70 -
Rwork0.281 1472 -
obs--99.87 %

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