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- PDB-7lsc: Crystal structure of near-infrared fluorescent protein miRFP670nano3 -

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Basic information

Entry
Database: PDB / ID: 7lsc
TitleCrystal structure of near-infrared fluorescent protein miRFP670nano3
ComponentsmiRFP670nano3
KeywordsFLUORESCENT PROTEIN / near-infrared fluorescent protein / miRFP / miRFPnano / phytochrome / BphP / cyanobacterichrome / CBCR
Function / homologyChem-JRA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletnev, S.
CitationJournal: To Be Published
Title: Near-infrared fluorescent protein with enhanced brightness.
Authors: Pletnev, S.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: miRFP670nano3
B: miRFP670nano3
C: miRFP670nano3
D: miRFP670nano3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6938
Polymers75,3544
Non-polymers2,3394
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-32 kcal/mol
Surface area26990 Å2
Unit cell
Length a, b, c (Å)111.531, 73.953, 83.743
Angle α, β, γ (deg.)90.000, 101.710, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1026-

HOH

21B-1106-

HOH

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Components

#1: Protein
miRFP670nano3


Mass: 18838.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-JRA / 3-[2-[(~{Z})-[5-[(~{Z})-[(3~{S},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 584.662 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 8.4% PEG4000, 3.6% MPD, 0.06 M sodium/potassium phosphate, pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 60575 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 0.657 / Net I/σ(I): 9.8 / Num. measured all: 274220
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.90.81557340.6820.4460.9350.42593.6
1.86-1.944.40.5660340.8530.2850.6320.45399.3
1.94-2.034.60.39461440.920.1990.4440.4899.7
2.03-2.134.70.28360930.9520.1420.3180.55399.7
2.13-2.274.60.19260910.9740.0980.2170.61699.5
2.27-2.444.50.1460800.9830.0710.1580.70498.8
2.44-2.694.30.09859400.9910.0510.1110.75996.4
2.69-3.084.90.07261380.9950.0350.080.78299.9
3.08-3.884.80.05661570.9970.0270.0630.83399.4
3.88-304.50.05261640.9940.0270.0590.8998.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MGH

6mgh


Resolution: 1.8→29.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.743 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1185 2 %RANDOM
Rwork0.1778 ---
obs0.1789 59390 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.36 Å2 / Biso mean: 38.314 Å2 / Biso min: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-2.14 Å2
2---0.32 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.8→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 172 371 5483
Biso mean--79.25 47.22 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135240
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174825
X-RAY DIFFRACTIONr_angle_refined_deg2.2831.697124
X-RAY DIFFRACTIONr_angle_other_deg1.5341.61111101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7075602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22522.23296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72715894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1251537
X-RAY DIFFRACTIONr_chiral_restr0.0960.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025872
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021195
LS refinement shellResolution: 1.802→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 85 -
Rwork0.301 3955 -
all-4040 -
obs--89.12 %

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