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- PDB-7lsd: Crystal structure of near-infrared fluorescent protein miRFP718nano -

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Basic information

Entry
Database: PDB / ID: 7lsd
TitleCrystal structure of near-infrared fluorescent protein miRFP718nano
ComponentsmiRFP718nano
KeywordsFLUORESCENT PROTEIN / near-infrared fluorescent protein / miRFP / miRFPnano / phytochrome / BphP / cyanobacterichrome / CBCR
Function / homologyGAF domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / BILIVERDINE IX ALPHA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPletnev, S.
CitationJournal: To Be Published
Title: Rational design of a small near-infrared fluorescent protein from CBCR suitable for deep-tissue SWIR imaging.
Authors: Oliinyk, O.S. / Pletnev, S. / Ma, C. / Baloban, M. / Toboada, C. / Sheng, H. / Yao, J. / Verkhusha, V.V.
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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: miRFP718nano
B: miRFP718nano
C: miRFP718nano
D: miRFP718nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6448
Polymers75,3144
Non-polymers2,3314
Water13,655758
1
A: miRFP718nano
B: miRFP718nano
hetero molecules

C: miRFP718nano
D: miRFP718nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6448
Polymers75,3144
Non-polymers2,3314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)122.204, 103.198, 75.548
Angle α, β, γ (deg.)90.000, 125.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-1102-

HOH

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Components

#1: Protein
miRFP718nano


Mass: 18828.457 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-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 12.6% PEG6000, 0.1 M lithium sulfate, 0.07 M citric acid, pH 3.5, 2.1% D-sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / 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: 1.7→30 Å / Num. obs: 80892 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Χ2: 0.616 / Net I/σ(I): 10.3 / Num. measured all: 285750
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.763.40.62880190.7690.3950.7440.40396.4
1.76-1.833.30.38577430.8750.250.4620.41792.6
1.83-1.913.60.25980250.9520.1580.3040.45696.1
1.91-2.023.70.16581510.9790.10.1930.50597.7
2.02-2.143.60.11181730.9890.0680.1310.58498
2.14-2.313.50.0881930.9920.050.0940.65198
2.31-2.543.40.0681060.9940.0380.0710.71596.8
2.54-2.913.60.04979720.9960.030.0580.78895
2.91-3.663.60.0483110.9970.0240.0470.81998.8
3.66-303.50.03281990.9980.020.0370.78596.6

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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: 1.7→29.84 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.358 / SU ML: 0.074 / SU R Cruickshank DPI: 0.0893 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 1579 2 %RANDOM
Rwork0.1574 ---
obs0.1582 79313 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.38 Å2 / Biso mean: 26.701 Å2 / Biso min: 14.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-1.08 Å2
2---0.04 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 1.7→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 172 778 5869
Biso mean--23.89 43.11 -
Num. residues----605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135327
X-RAY DIFFRACTIONr_bond_other_d0.0110.0174829
X-RAY DIFFRACTIONr_angle_refined_deg2.3941.6837249
X-RAY DIFFRACTIONr_angle_other_deg1.9671.6111138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0622.718298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62815889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5871532
X-RAY DIFFRACTIONr_chiral_restr0.0890.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.026050
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021210
LS refinement shellResolution: 1.7→1.741 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.299 107 -
Rwork0.278 5784 -
obs--94.7 %

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