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- PDB-5yt1: Crystal structrure of near infrared fluoresecent protein mNeptune684 -

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Basic information

Entry
Database: PDB / ID: 5yt1
TitleCrystal structrure of near infrared fluoresecent protein mNeptune684
Componentsnear infrared fluoresecent protein mNeptune684
KeywordsFLUORESCENT PROTEIN / mNeptune / near infrared fluorescent protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, X.E. / Wang, D.B. / Yuan, Y. / Li, D.F.
CitationJournal: to be published
Title: Crystal structrure of near infrared fluoresecent protein mNeptune684
Authors: Zhang, X.E. / Wang, D.B. / Yuan, Y. / Li, D.F.
History
DepositionNov 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: near infrared fluoresecent protein mNeptune684
B: near infrared fluoresecent protein mNeptune684
C: near infrared fluoresecent protein mNeptune684
D: near infrared fluoresecent protein mNeptune684


Theoretical massNumber of molelcules
Total (without water)115,6724
Polymers115,6724
Non-polymers00
Water14,088782
1
A: near infrared fluoresecent protein mNeptune684


Theoretical massNumber of molelcules
Total (without water)28,9181
Polymers28,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: near infrared fluoresecent protein mNeptune684


Theoretical massNumber of molelcules
Total (without water)28,9181
Polymers28,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: near infrared fluoresecent protein mNeptune684


Theoretical massNumber of molelcules
Total (without water)28,9181
Polymers28,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: near infrared fluoresecent protein mNeptune684


Theoretical massNumber of molelcules
Total (without water)28,9181
Polymers28,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.643, 116.878, 63.721
Angle α, β, γ (deg.)90.00, 106.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
near infrared fluoresecent protein mNeptune684


Mass: 28917.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Strain: sea anemone / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20 mM Tris, NaCl 100 mM, pH 7.9, 0.2 M Lithium Chloride, 20% w/v Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2→46.81 Å / Num. obs: 60120 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.136 / Net I/σ(I): 10.41
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.557 / Num. unique obs: 4482 / CC1/2: 0.691 / Rrim(I) all: 0.607 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ip2

3ip2


Resolution: 2→46.802 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 22.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1986 3.3 %Random
Rwork0.1968 ---
obs0.1976 60120 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 0 782 7994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057388
X-RAY DIFFRACTIONf_angle_d1.0149985
X-RAY DIFFRACTIONf_dihedral_angle_d9.4114405
X-RAY DIFFRACTIONf_chiral_restr0.0571052
X-RAY DIFFRACTIONf_plane_restr0.0051293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32681430.26944178X-RAY DIFFRACTION100
2.05-2.10540.28151380.23924095X-RAY DIFFRACTION100
2.1054-2.16740.2411390.2324112X-RAY DIFFRACTION100
2.1674-2.23740.25861420.24774136X-RAY DIFFRACTION100
2.2374-2.31730.26581440.25384160X-RAY DIFFRACTION100
2.3173-2.41010.24661440.21334128X-RAY DIFFRACTION100
2.4101-2.51980.27421410.21354150X-RAY DIFFRACTION100
2.5198-2.65260.23611430.20494179X-RAY DIFFRACTION100
2.6526-2.81880.23381380.20614121X-RAY DIFFRACTION100
2.8188-3.03640.2571450.21124187X-RAY DIFFRACTION100
3.0364-3.34190.21841430.19494144X-RAY DIFFRACTION100
3.3419-3.82530.19951450.17024129X-RAY DIFFRACTION100
3.8253-4.81870.16851400.15474190X-RAY DIFFRACTION100
4.8187-46.81470.16711410.17074225X-RAY DIFFRACTION100

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