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- PDB-4ryw: Crystal structure of the photoconverted green fluorescent protein... -

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Basic information

Entry
Database: PDB / ID: 4ryw
TitleCrystal structure of the photoconverted green fluorescent protein NowGFP_conv (the variant of cyan Cerulean) at pH 7.0
ComponentsNowGFP_conv
KeywordsFLUORESCENT PROTEIN / photoconverted NowGFP / TWG chromophore / beta-barrel / variant of cyan Cerulean
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore.
Authors: Pletnev, V.Z. / Pletneva, N.V. / Sarkisyan, K.S. / Mishin, A.S. / Lukyanov, K.A. / Goryacheva, E.A. / Ziganshin, R.H. / Dauter, Z. / Pletnev, S.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NowGFP_conv
B: NowGFP_conv
C: NowGFP_conv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,73712
Polymers83,9083
Non-polymers8299
Water2,954164
1
A: NowGFP_conv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1543
Polymers27,9691
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NowGFP_conv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3385
Polymers27,9691
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NowGFP_conv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2464
Polymers27,9691
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.132, 98.021, 71.671
Angle α, β, γ (deg.)90.000, 111.630, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThree molecules in the assymetric unit

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Components

#1: Protein NowGFP_conv


Mass: 27969.389 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThis construct is a gene engineered variant of the cyan fluorescent protein Cerulean

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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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Na Acetate pH=4.5, 30% (v/v) PEG 5000 mono methyl ether, pH 7.0, 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: 2014 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23175 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.117 / Χ2: 0.856 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.60.50223120.756199.9
2.59-2.693.60.41223080.7671100
2.69-2.823.70.32522830.8091100
2.82-2.963.70.25223150.811100
2.96-3.153.80.17823200.8941100
3.15-3.393.80.13623160.9721100
3.39-3.733.80.10923141.0741100
3.73-4.273.80.09123041.063199.9
4.27-5.383.80.07123280.8681100
5.38-303.70.05723750.531100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WSO

2wso


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.2862 / WRfactor Rwork: 0.2033 / FOM work R set: 0.769 / SU B: 13.06 / SU ML: 0.297 / SU Rfree: 0.3815 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 1182 5.1 %RANDOM
Rwork0.2051 ---
obs0.2097 21817 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.95 Å2 / Biso mean: 37.682 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.14 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 54 164 5645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195610
X-RAY DIFFRACTIONr_bond_other_d0.0030.025292
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9827562
X-RAY DIFFRACTIONr_angle_other_deg0.765312250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47925.251259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32815966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2251518
X-RAY DIFFRACTIONr_chiral_restr0.080.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021245
X-RAY DIFFRACTIONr_mcbond_it2.3183.6182728
X-RAY DIFFRACTIONr_mcbond_other2.3183.6162727
X-RAY DIFFRACTIONr_mcangle_it3.6185.4193398
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 60 -
Rwork0.258 1440 -
all-1500 -
obs--86.91 %

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