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- PDB-4n3d: Crystal structure of the dimeric variant EGFP-K162Q in P61 space group -

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Basic information

Entry
Database: PDB / ID: 4n3d
TitleCrystal structure of the dimeric variant EGFP-K162Q in P61 space group
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / EGFP / green fluorescent protein / beta-barrel / Thr-Tyr-Gly chromophore / Fluorescent biomarker
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsPletneva, N.V. / Pletnev, V.Z. / Pletnev, S.V.
CitationJournal: Rus.J.Bioorg.Chem. / Year: 2014
Title: Three dimensional structure of the dimeric gene-engineered variant of green fluorescent protein egfp-K162Q in P61 crystal space group
Authors: Pletneva, N.V. / V Pletnev, S. / Bogdanov, A.M. / Goryacheva, E.A. / Artemyev, I.V. / Souslova, E.A. / Arkhipova, S.F. / Pletnev, V.Z.
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,48110
Polymers54,8982
Non-polymers5848
Water9,890549
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0329
Polymers27,4491
Non-polymers5848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,4491
Polymers27,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.861, 121.861, 64.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Green fluorescent protein /


Mass: 27448.816 Da / Num. of mol.: 2 / Mutation: K162Q, H231L
Source method: isolated from a genetically manipulated source
Details: EGFP-K162Q / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Two microliters of protein 10mg/ml in buffer 20 Tris 8.0 100 NaCl mixed with equal amount of resevoir solution - 0.056 NaH2PO4, 1.344 M K2HPO4 pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: 2013 / Details: mirrors
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 122157 / % possible obs: 99.3 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Χ2: 0.835 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.34-1.396.60.659113820.771193.3
1.39-1.447.40.514122800.7721100
1.44-1.517.40.351122590.7681100
1.51-1.597.50.228122590.781100
1.59-1.697.50.16122690.8181100
1.69-1.827.50.108122670.8521100
1.82-27.60.068123010.9051100
2-2.297.60.062122860.8221100
2.29-2.897.70.066123520.7731100
2.89-507.60.026125021.064199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→22.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.1836 / Occupancy max: 1 / FOM work R set: 0.8897 / SU R Cruickshank DPI: 0.05 / SU Rfree: 0.0497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1231 1 %RANDOM
Rwork0.1806 ---
obs0.1807 122019 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.77 Å2 / Biso mean: 18.3799 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.34→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 31 549 4200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223923
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9765342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78425.344189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04915691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1831513
X-RAY DIFFRACTIONr_chiral_restr0.1510.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213019
X-RAY DIFFRACTIONr_mcbond_it1.5481.52349
X-RAY DIFFRACTIONr_mcangle_it2.51823835
X-RAY DIFFRACTIONr_scbond_it3.41931574
X-RAY DIFFRACTIONr_scangle_it5.4584.51489
LS refinement shellResolution: 1.343→1.377 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 98 -
Rwork0.264 8801 -
all-8899 -
obs--99.71 %

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