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- PDB-6mgh: X-ray structure of monomeric near-infrared fluorescent protein mi... -

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Basic information

Entry
Database: PDB / ID: 6mgh
TitleX-ray structure of monomeric near-infrared fluorescent protein miRFP670nano
ComponentsmiRFP670nano
KeywordsFLUORESCENT PROTEIN / NEAR-INFRARED FLUORESCENT PROTEIN / GAF DOMAIN / CYANOBACTERIOCHROME FP
Function / homologyGAF domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / Chem-JRA
Function and homology information
Biological speciesAcaryochloris marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPletnev, S.
CitationJournal: Nat Commun / Year: 2019
Title: Smallest near-infrared fluorescent protein evolved from cyanobacteriochrome as versatile tag for spectral multiplexing.
Authors: Oliinyk, O.S. / Shemetov, A.A. / Pletnev, S. / Shcherbakova, D.M. / Verkhusha, V.V.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: miRFP670nano
B: miRFP670nano
C: miRFP670nano
D: miRFP670nano
E: miRFP670nano
F: miRFP670nano
G: miRFP670nano
H: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,74522
Polymers150,5798
Non-polymers5,16614
Water10,503583
1
A: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4072
Polymers18,8221
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5594
Polymers18,8221
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5594
Polymers18,8221
Non-polymers7373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4072
Polymers18,8221
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4072
Polymers18,8221
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4072
Polymers18,8221
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4993
Polymers18,8221
Non-polymers6772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: miRFP670nano
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4993
Polymers18,8221
Non-polymers6772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.598, 72.124, 136.698
Angle α, β, γ (deg.)90.000, 129.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
miRFP670nano


Mass: 18822.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acaryochloris marina (bacteria) / 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.: 8 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M Na Acetate pH 4.0, 10mM EDTA, 10% isopropanol, 22% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 100484 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.058 / Rrim(I) all: 0.113 / Χ2: 0.935 / Net I/σ(I): 7.8 / Num. measured all: 376413
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.023.30.55798750.7620.3530.6610.66597.6
2.02-2.13.70.45899380.8450.2780.5360.71497.8
2.1-2.23.80.34999230.9070.2070.4060.78398
2.2-2.313.80.272100080.9470.160.3160.85498.2
2.31-2.463.80.21999930.9620.1290.2540.92898.4
2.46-2.653.80.162100460.9740.0960.1890.96598.6
2.65-2.913.80.118100470.9840.070.1381.01298.7
2.91-3.333.80.087101240.990.0510.1011.06299
3.33-4.23.80.06101760.9930.0360.071.13799.2
4.2-303.70.045103540.9960.0270.0531.16199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.524 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1106 1.1 %RANDOM
Rwork0.1825 ---
obs0.1831 99377 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.15 Å2 / Biso mean: 26.903 Å2 / Biso min: 9.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.82 Å2
2--0.4 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9697 0 376 584 10657
Biso mean--30.02 32.99 -
Num. residues----1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910283
X-RAY DIFFRACTIONr_bond_other_d0.0040.029841
X-RAY DIFFRACTIONr_angle_refined_deg2.4151.96114003
X-RAY DIFFRACTIONr_angle_other_deg1.215322349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38151180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03624.063512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.223151717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7691580
X-RAY DIFFRACTIONr_chiral_restr0.1470.21554
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211652
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022588
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 85 -
Rwork0.258 7202 -
all-7287 -
obs--97.2 %

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