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- PDB-5exb: Wild type green fluorescent protein DendFP (Dendronephthya sp.) -

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Basic information

Entry
Database: PDB / ID: 5exb
TitleWild type green fluorescent protein DendFP (Dendronephthya sp.)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Photoswitchable fluorescent proteins / chromophore / beta-barrel / biomarker
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
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 speciesDendronephthya sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00281 Russian Federation
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.
Authors: Pletneva, N.V. / Pletnev, S. / Pakhomov, A.A. / Chertkova, R.V. / Martynov, V.I. / Muslinkina, L. / Dauter, Z. / Pletnev, V.Z.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Revision 1.4Sep 8, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein
G: Green fluorescent protein
H: Green fluorescent protein
I: Green fluorescent protein
J: Green fluorescent protein
K: Green fluorescent protein
L: Green fluorescent protein
M: Green fluorescent protein
N: Green fluorescent protein
O: Green fluorescent protein
P: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,93119
Polymers429,65416
Non-polymers2763
Water34,5531918
1
A: Green fluorescent protein
D: Green fluorescent protein
F: Green fluorescent protein
O: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)107,4144
Polymers107,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
C: Green fluorescent protein
E: Green fluorescent protein
P: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5986
Polymers107,4144
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Green fluorescent protein
I: Green fluorescent protein
K: Green fluorescent protein
N: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5065
Polymers107,4144
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Green fluorescent protein
J: Green fluorescent protein
L: Green fluorescent protein
M: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)107,4144
Polymers107,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.384, 106.397, 137.209
Angle α, β, γ (deg.)109.680, 100.010, 101.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Green fluorescent protein /


Mass: 26853.391 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendronephthya sp. (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T6U0
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1918 / 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: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Mg formate, 20% PEG 3350

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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: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 310150 / % possible obs: 97 % / Redundancy: 2 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.046 / Χ2: 0.82 / Net I/av σ(I): 19.568 / Net I/σ(I): 13.5 / Num. measured all: 615189
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.841.90.244144590.8090.2440.3450.83990.6
1.84-1.8720.217153920.8380.2170.3070.84995.8
1.87-1.9120.18152810.8980.180.2550.88796
1.91-1.9520.158153320.90.1580.2240.9596.1
1.95-1.9920.133154760.9340.1330.1880.98496.3
1.99-2.0420.109154400.9570.1090.1550.97996.5
2.04-2.0920.096154360.9620.0960.1360.9996.6
2.09-2.1520.084154160.9690.0840.1191.01196.8
2.15-2.2120.074154720.9760.0740.1041.00796.9
2.21-2.2820.069155450.9790.0690.0981.02797.1
2.28-2.3620.062155260.9830.0620.0880.95297.3
2.36-2.4620.052156590.9880.0520.0740.9197.5
2.46-2.5720.045156040.9880.0450.0640.83297.7
2.57-2.720.038155810.9910.0380.0540.79897.9
2.7-2.8720.033157220.9930.0330.0470.72498.1
2.87-3.0920.03156850.9930.030.0420.6698.2
3.09-3.4120.027157570.9950.0260.0370.64998.4
3.41-3.920.025157160.9950.0250.0350.60898.7
3.9-4.9120.022158830.9960.0220.030.49599
4.91-5020.016157680.9980.0160.0230.25798.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 1.81→37.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 3215 1 %RANDOM
Rwork0.1821 ---
obs0.1828 306888 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.72 Å2 / Biso mean: 22.043 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.12 Å20.04 Å2
2---0.09 Å20.03 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.81→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29036 0 18 1918 30972
Biso mean--22.64 23.85 -
Num. residues----3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01930109
X-RAY DIFFRACTIONr_bond_other_d00.0228029
X-RAY DIFFRACTIONr_angle_refined_deg2.2241.97340819
X-RAY DIFFRACTIONr_angle_other_deg3.844364804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.41153575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30924.3831435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.344155131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.74615133
X-RAY DIFFRACTIONr_chiral_restr0.1320.24225
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02133910
X-RAY DIFFRACTIONr_gen_planes_other0.020.027007
X-RAY DIFFRACTIONr_mcbond_it2.0082.15914294
X-RAY DIFFRACTIONr_mcbond_other2.0082.15814293
X-RAY DIFFRACTIONr_mcangle_it2.9163.22717843
LS refinement shellResolution: 1.806→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 178 -
Rwork0.23 17492 -
all-17670 -
obs--74.81 %

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