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- PDB-4eds: Crystal structure of far-red fluorescent protein eqFP670 -

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Basic information

Entry
Database: PDB / ID: 4eds
TitleCrystal structure of far-red fluorescent protein eqFP670
Componentsfar-red fluorescent protein eqFP650
KeywordsFLUORESCENT PROTEIN / beta barrel
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Far-red fluorescent protein eqFP650
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPletnev, S. / Pletnev, V.Z. / Pletneva, N.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670.
Authors: Pletnev, S. / Pletneva, N.V. / Souslova, E.A. / Chudakov, D.M. / Lukyanov, S. / Wlodawer, A. / Dauter, Z. / Pletnev, V.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: far-red fluorescent protein eqFP650
B: far-red fluorescent protein eqFP650


Theoretical massNumber of molelcules
Total (without water)54,6662
Polymers54,6662
Non-polymers00
Water6,485360
1
A: far-red fluorescent protein eqFP650


Theoretical massNumber of molelcules
Total (without water)27,3331
Polymers27,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: far-red fluorescent protein eqFP650


Theoretical massNumber of molelcules
Total (without water)27,3331
Polymers27,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: far-red fluorescent protein eqFP650
B: far-red fluorescent protein eqFP650

A: far-red fluorescent protein eqFP650
B: far-red fluorescent protein eqFP650


Theoretical massNumber of molelcules
Total (without water)109,3324
Polymers109,3324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area10420 Å2
ΔGint-34 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.605, 104.605, 214.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein far-red fluorescent protein eqFP650


Mass: 27332.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: J9PBR8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 3.1 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 M Na Acetate, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 92328 / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.059 / Χ2: 0.954 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6612.40.51590640.8021100
1.66-1.7217.40.37190850.8181100
1.72-1.821.90.26991100.8481100
1.8-1.9220.17291090.9091100
1.9-2.02220.11191560.971100
2.02-2.1722.10.08891351.0391100
2.17-2.3922.10.08592351.0391100
2.39-2.74220.06292471.0681100
2.74-3.4521.80.05993510.985199.9
3.45-3020.70.04298360.955199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.4_156refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.903 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8715 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 4619 5.01 %
Rwork0.1796 --
obs0.1805 92226 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.729 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 75.46 Å2 / Biso mean: 24.4108 Å2 / Biso min: 9.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.0363 Å20 Å2-0 Å2
2--1.0363 Å20 Å2
3----2.0727 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 0 360 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134088
X-RAY DIFFRACTIONf_angle_d1.5785584
X-RAY DIFFRACTIONf_chiral_restr0.113565
X-RAY DIFFRACTIONf_plane_restr0.007756
X-RAY DIFFRACTIONf_dihedral_angle_d17.571547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61590.28281630.2382821298499
1.6159-1.6350.2281360.216528873023100
1.635-1.65490.21791700.206628383008100
1.6549-1.67580.26911370.204629103047100
1.6758-1.69790.25071540.205328513005100
1.6979-1.72110.21521480.194128883036100
1.7211-1.74570.23851450.190729043049100
1.7457-1.77180.20111430.196928743017100
1.7718-1.79950.21271480.203228923040100
1.7995-1.8290.25171450.192928763021100
1.829-1.86050.22871460.199328913037100
1.8605-1.89430.23151470.196929153062100
1.8943-1.93080.2041670.197328593026100
1.9308-1.97020.20051420.196529113053100
1.9702-2.0130.22721620.183629033065100
2.013-2.05980.19671510.18328803031100
2.0598-2.11130.19181430.179229143057100
2.1113-2.16840.2031450.18529043049100
2.1684-2.23220.2221710.18529123083100
2.2322-2.30420.20551480.186929053053100
2.3042-2.38650.20191430.183629493092100
2.3865-2.4820.21581500.184129233073100
2.482-2.59490.1971750.183528963071100
2.5949-2.73160.19861700.186629293099100
2.7316-2.90260.21681630.185229503113100
2.9026-3.12650.21881680.192329503118100
3.1265-3.44080.18371600.170929573117100
3.4408-3.93770.19381560.149930233179100
3.9377-4.95740.12791590.128230483207100
4.9574-29.9030.1691640.173432473411100

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