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- PDB-4rys: Crystal structure of the green fluorescent rotein NowGFP (the var... -

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Basic information

Entry
Database: PDB / ID: 4rys
TitleCrystal structure of the green fluorescent rotein NowGFP (the variant of cyan Cerulean) at pH 4.8
ComponentsNowGFP
KeywordsFLUORESCENT PROTEIN / NowGFP / TWG chromophore / beta-barrel / variant of cyan Cerulean
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesCFP MARKER PLASMID PWM1009 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NowGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7577
Polymers27,2051
Non-polymers5536
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.589, 51.274, 60.997
Angle α, β, γ (deg.)90.000, 108.280, 90.000
Int Tables number5
Space group name H-MC121
DetailsOne monomer in assymetric unit

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Components

#1: Protein NowGFP


Mass: 27204.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CFP MARKER PLASMID PWM1009 (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 14mM KH2PO4, pH 4.8, 14% PEG3350, 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: 1.18→50 Å / Num. obs: 107191 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.904 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.18-1.2230.425103850.834196.8
1.22-1.273.50.35106580.832199.6
1.27-1.333.60.269107000.846199.7
1.33-1.43.70.218107120.873199.9
1.4-1.493.70.154107300.9021100
1.49-1.63.70.102107290.931100
1.6-1.763.70.078107640.9921100
1.76-2.023.80.07107740.9061100
2.02-2.543.80.06108260.971100
2.54-503.70.037109130.92199.4

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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: 1.18→26.19 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1465 / WRfactor Rwork: 0.133 / FOM work R set: 0.9091 / SU R Cruickshank DPI: 0.026 / SU Rfree: 0.0252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1425 1593 1.5 %RANDOM
Rwork0.1316 ---
obs0.1318 105595 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.06 Å2 / Biso mean: 15.798 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2--0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.18→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 36 326 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192067
X-RAY DIFFRACTIONr_bond_other_d00.021964
X-RAY DIFFRACTIONr_angle_refined_deg3.1562.0012812
X-RAY DIFFRACTIONr_angle_other_deg3.8434574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0675268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80525.37693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69515365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.788157
X-RAY DIFFRACTIONr_chiral_restr0.2510.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212351
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02456
X-RAY DIFFRACTIONr_mcbond_it1.2541.191981
X-RAY DIFFRACTIONr_mcbond_other1.2681.187980
X-RAY DIFFRACTIONr_mcangle_it1.4621.7981239
X-RAY DIFFRACTIONr_rigid_bond_restr15.52134031
X-RAY DIFFRACTIONr_sphericity_free53.87587
X-RAY DIFFRACTIONr_sphericity_bonded9.37854213
LS refinement shellResolution: 1.179→1.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 106 -
Rwork0.224 7369 -
all-7475 -
obs--94.49 %

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