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- PDB-3ip2: Crystal structure of red fluorescent protein Neptune at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 3ip2
TitleCrystal structure of red fluorescent protein Neptune at pH 7.0
ComponentsNeptune red fluorescent protein
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLin, M.Z. / McKeown, M.R. / Ng, H.L. / Aguilera, T.A. / Shaner, N.C. / Ma, W. / Adams, S.R. / Campbell, R.E. / Alber, T. / Tsien, R.Y.
CitationJournal: Chem.Biol. / Year: 2009
Title: Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals.
Authors: Lin, M.Z. / McKeown, M.R. / Ng, H.L. / Aguilera, T.A. / Shaner, N.C. / Campbell, R.E. / Adams, S.R. / Gross, L.A. / Ma, W. / Alber, T. / Tsien, R.Y.
History
DepositionAug 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neptune red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,3691
Polymers27,3691
Non-polymers00
Water3,819212
1
A: Neptune red fluorescent protein

A: Neptune red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)54,7382
Polymers54,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area4410 Å2
ΔGint-23 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.144, 92.144, 53.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

Detailsauthors state that this is a WEAK DIMER (DISSOCIATION CONSTANT 500 NANOMOLAR).

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Components

#1: Protein Neptune red fluorescent protein


Mass: 27369.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES MET 63, TYR 64 AND GLY 65 AUTOCATALYTICALLY FORM THE CHROMOPHORE NRQ LABELLED AS RESIDUE ...RESIDUES MET 63, TYR 64 AND GLY 65 AUTOCATALYTICALLY FORM THE CHROMOPHORE NRQ LABELLED AS RESIDUE 63 IN THE COORDINATES.

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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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 uL of protein at 10 mg/mL was mixed with 1 uL of 0.1 M HEPES, 0.2 M CaCl2, 20% PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11586 Å / Relative weight: 1
ReflectionResolution: 1.6→92.1 Å / Num. all: 30810 / Num. obs: 30755 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rsym value: 0.055 / Net I/σ(I): 23.8
Reflection shellResolution: 1.6→1.68 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 4369 / Rsym value: 0.778 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3BXA

3bxa


Resolution: 1.6→65.2 Å / SU ML: 0.27 / σ(F): -3 / Stereochemistry target values: Engh & Huber / Details: TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1547 5.03 %random 5%
Rwork0.1713 ---
obs0.1728 30735 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.022 Å2 / ksol: 0.42 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 212 2033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65170.28251420.26142577X-RAY DIFFRACTION100
1.6517-1.71070.28341440.22982582X-RAY DIFFRACTION100
1.7107-1.77920.20971220.19912644X-RAY DIFFRACTION100
1.7792-1.86020.24781450.17342582X-RAY DIFFRACTION100
1.8602-1.95820.21121290.16612648X-RAY DIFFRACTION100
1.9582-2.08090.19011300.15152641X-RAY DIFFRACTION100
2.0809-2.24160.19481430.15122661X-RAY DIFFRACTION100
2.2416-2.46720.19991540.15422649X-RAY DIFFRACTION100
2.4672-2.82420.19371610.15682641X-RAY DIFFRACTION100
2.8242-3.55820.18341430.15042717X-RAY DIFFRACTION100
3.5582-65.20980.18071340.16672866X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.8391 Å / Origin y: 21.7715 Å / Origin z: 25.2752 Å
111213212223313233
T0.1193 Å2-0.0047 Å20.0788 Å2-0.0729 Å2-0.0156 Å2--0.1944 Å2
L2.3581 °2-0.3917 °2-0.2164 °2-1.6124 °2-0.193 °2--0.4955 °2
S0.1052 Å °0.013 Å °0.5749 Å °-0.0876 Å °0.0287 Å °-0.1846 Å °-0.0872 Å °-0.0176 Å °-0.1362 Å °
Refinement TLS groupSelection details: chain A

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