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- PDB-3m22: Crystal structure of TagRFP fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 3m22
TitleCrystal structure of TagRFP fluorescent protein
ComponentsTagRFP
KeywordsDE NOVO PROTEIN / Acylimine-containing blue and red chromophores / tagrfp / fluorescent proteins
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Subach, O.M. / Ramagopal, U.A. / Almo, S.C. / Verkhusha, V.V.
CitationJournal: Chem.Biol. / Year: 2010
Title: Structural characterization of acylimine-containing blue and red chromophores in mTagBFP and TagRFP fluorescent proteins.
Authors: Subach, O.M. / Malashkevich, V.N. / Zencheck, W.D. / Morozova, K.S. / Piatkevich, K.D. / Almo, S.C. / Verkhusha, V.V.
History
DepositionMar 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TagRFP
B: TagRFP
C: TagRFP
D: TagRFP


Theoretical massNumber of molelcules
Total (without water)106,9904
Polymers106,9904
Non-polymers00
Water11,926662
1
A: TagRFP


Theoretical massNumber of molelcules
Total (without water)26,7481
Polymers26,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TagRFP


Theoretical massNumber of molelcules
Total (without water)26,7481
Polymers26,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TagRFP


Theoretical massNumber of molelcules
Total (without water)26,7481
Polymers26,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TagRFP


Theoretical massNumber of molelcules
Total (without water)26,7481
Polymers26,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: TagRFP
B: TagRFP


Theoretical massNumber of molelcules
Total (without water)53,4952
Polymers53,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-20 kcal/mol
Surface area18170 Å2
MethodPISA
6
C: TagRFP
D: TagRFP


Theoretical massNumber of molelcules
Total (without water)53,4952
Polymers53,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-22 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.989, 130.989, 105.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-348-

HOH

21C-312-

HOH

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Components

#1: Protein
TagRFP


Mass: 26747.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 30% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 0.1 M TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2008
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 50406 / % possible obs: 85.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 3.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.371 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2269 5.3 %RANDOM
Rwork0.16 ---
obs0.161 40866 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2--2.21 Å20 Å2
3----4.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 0 662 7834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9849931
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55624.337332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.847151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0711536
X-RAY DIFFRACTIONr_chiral_restr0.10.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6943.54404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.321507108
X-RAY DIFFRACTIONr_scbond_it7.711502959
X-RAY DIFFRACTIONr_scangle_it0.6034.52819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 111 -
Rwork0.132 2156 -
obs--68.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05590.0225-0.04360.0188-0.00820.2219-0.0055-0.02240.0175-0.01690.00450.0108-0.03350.01280.0010.0508-0.00220.00350.03330.0020.042816.215814.232830.6598
20.05950.0095-0.01720.13710.01060.02450.0120.00010.01360.0180.00160.00850.01060.0091-0.01370.05050.0021-0.00380.0395-0.00230.04216.1785-14.505222.3063
30.014-0.04350.00470.1978-0.07030.06680.00430.00790.00510.02760.0072-0.0212-0.0315-0.0163-0.01160.05240.0028-0.00570.0431-0.00220.039949.236714.257848.7984
40.1374-0.0305-0.00770.0472-0.06230.11760.0098-0.00880.0035-0.02030.0008-0.0010.0385-0.0209-0.01060.05120.0002-0.00460.03410.00760.038949.4084-14.511857.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 228
2X-RAY DIFFRACTION2B3 - 228
3X-RAY DIFFRACTION3C3 - 228
4X-RAY DIFFRACTION4D3 - 228

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