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- PDB-5dqb: Green/cyan WasCFP at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 5dqb
TitleGreen/cyan WasCFP at pH 8.0
ComponentsWasCFP_pH2
KeywordsFLUORESCENT PROTEIN / Cyan fluorescent protein / Trp based chromophore / temperature and pH dependence / Cerulean variant
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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea coerulescens (belt jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPletnev, V. / Pletneva, N. / Pletnev, S.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian fund for basic research14-04-00004 Russian Federation
Molecular Cell Biology fund Russian Federation
CitationJournal: Russ.J.Bioorganic Chem. / Year: 2016
Title: Crystal structure of pH and T dependent green fluorescent protein WasCFP with Trp based chromophore
Authors: Pletnev, V.Z. / Pletneva, N. / Efremov, R.G. / Goryacheva, E.A. / Artemyev, I.V. / Arkhipova, S.F. / Sarkisyan, K.S. / Mishin, A.S. / Lukyanov, K.A. / Pletnev, S.V.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WasCFP_pH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1753
Polymers28,0601
Non-polymers1152
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-16 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.401, 51.370, 50.033
Angle α, β, γ (deg.)90.000, 103.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WasCFP_pH2


Mass: 28059.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea coerulescens (belt jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Citric acid pH 5.5, 1 M LiCl, 30 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 63293 / % possible obs: 96.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Χ2: 1.03 / Net I/av σ(I): 14.042 / Net I/σ(I): 9.1 / Num. measured all: 237198
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.25-1.293.60.56260700.96193.3
1.29-1.353.70.47161741.00594.1
1.35-1.413.80.38562241.06594.9
1.41-1.483.70.2862191.07795.3
1.48-1.573.80.20162951.11195.8
1.57-1.73.80.14963331.08296.5
1.7-1.873.80.12364061.06697.2
1.87-2.143.80.10264190.99497.6
2.14-2.693.80.08665340.96698.6
2.69-303.70.05166190.96798.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.5.010refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2361 / WRfactor Rwork: 0.1856 / FOM work R set: 0.8188 / SU R Cruickshank DPI: 0.0522 / SU Rfree: 0.0556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1277 2 %RANDOM
Rwork0.1792 ---
obs0.1802 61910 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.28 Å2 / Biso mean: 15.025 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.3 Å2
2---0.64 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 7 313 2136
Biso mean--29.48 30.07 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221931
X-RAY DIFFRACTIONr_angle_refined_deg2.4411.9932626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68225.60491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7515335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.611156
X-RAY DIFFRACTIONr_chiral_restr0.1580.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211488
X-RAY DIFFRACTIONr_mcbond_it2.7391.51157
X-RAY DIFFRACTIONr_mcangle_it3.59521879
X-RAY DIFFRACTIONr_scbond_it5.0143774
X-RAY DIFFRACTIONr_scangle_it7.1884.5740
X-RAY DIFFRACTIONr_rigid_bond_restr2.82631931
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 90 -
Rwork0.294 4339 -
all-4429 -
obs--90.93 %

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