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- PDB-7lug: Crystal structure of the pnRFP B30Y mutant -

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Basic information

Entry
Database: PDB / ID: 7lug
TitleCrystal structure of the pnRFP B30Y mutant
ComponentsRed Fluorescent pnRFP B30Y mutant
KeywordsFLUORESCENT PROTEIN / Red fluorescent protein / Peroxynitrite / Biosensor / Boronophenylalanine.
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHuang, M. / Ng, H.L. / Pang, Y. / Zhang, S. / Fan, Y. / Yeh, H. / Xiong, Y. / Li, X. / Ai, H.
CitationJournal: To Be Published
Title: Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor
Authors: Pang, Y. / Huang, M. / Zhang, S. / Fan, Y. / Yeh, H. / Xiong, Y. / Li, X. / Ng, H.L. / Ai, H.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 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: Red Fluorescent pnRFP B30Y mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8372
Polymers29,7421
Non-polymers951
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.284, 34.107, 89.222
Angle α, β, γ (deg.)90.000, 110.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Red Fluorescent pnRFP B30Y mutant


Mass: 29741.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia phage EcSzw-2 (virus)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: Sodium phosphate, citric acid, PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.95→41.85 Å / Num. obs: 17539 / % possible obs: 99.3 % / Redundancy: 3.56 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1245 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LQO

7lqo


Resolution: 1.95→41.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.451 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 886 5.1 %RANDOM
Rwork0.1885 ---
obs0.1897 16652 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.16 Å2 / Biso mean: 32.588 Å2 / Biso min: 22.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.09 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.95→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 5 65 1869
Biso mean--61.75 44.1 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171769
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6672558
X-RAY DIFFRACTIONr_angle_other_deg1.2121.5994106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68722.57797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24915327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.251510
X-RAY DIFFRACTIONr_chiral_restr0.0620.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022135
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02433
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 62 -
Rwork0.227 1241 -
all-1303 -
obs--99.39 %

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