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- PDB-6u1a: Crystal Structure of Fluorescent Protein FusionRed -

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Basic information

Entry
Database: PDB / ID: 6u1a
TitleCrystal Structure of Fluorescent Protein FusionRed
ComponentsRed fluorescent protein
KeywordsFLUORESCENT PROTEIN / alternative routes of post-translational modifications / hydrolysis
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / NICKEL (II) ION
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsPletnev, S. / Muslinkina, L. / Pletneva, N. / Pletnev, V.Z.
Funding support United States, Russian Federation, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
Russian Foundation for Basic Research19-04-00107 Russian Federation
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Two independent routes of post-translational chemistry in fluorescent protein FusionRed.
Authors: Muslinkina, L. / Pletnev, V.Z. / Pletneva, N.V. / Ruchkin, D.A. / Kolesov, D.V. / Bogdanov, A.M. / Kost, L.A. / Rakitina, T.V. / Agapova, Y.K. / Shemyakina, I.I. / Chudakov, D.M. / Pletnev, S.
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8816
Polymers25,6061
Non-polymers2755
Water6,575365
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)45.015, 55.261, 89.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Red fluorescent protein


Mass: 25605.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5 mM CoCl2, 5 mM NiCl2, 5mM CdCl2, 5mM MgCl2, 0.1 M HEPES pH 7.5, 12% PEG3350

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→30 Å / Num. obs: 92579 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Χ2: 0.988 / Net I/σ(I): 12.2 / Num. measured all: 633565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.09-1.135.50.56885780.8460.250.6230.71692.5
1.13-1.176.60.41492360.9290.170.4480.763100
1.17-1.236.90.3192740.9640.1250.3340.818100
1.23-1.2970.23292830.9790.0930.2510.877100
1.29-1.377.10.17192880.9870.0680.1841.007100
1.37-1.487.20.11992890.9930.0470.1291.078100
1.48-1.637.20.07993720.9970.0310.0861.133100
1.63-1.867.30.06593960.9970.0260.071.187100
1.86-2.356.60.04693110.9990.0190.051.12798.4
2.35-306.80.03695520.9980.0150.0391.05897.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BXA

3bxa


Resolution: 1.09→27.52 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.882 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 1861 2 %RANDOM
Rwork0.1267 ---
obs0.1271 90642 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 207.39 Å2 / Biso mean: 16.38 Å2 / Biso min: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--0.59 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.09→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 5 366 2118
Biso mean--17.37 30.96 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0132041
X-RAY DIFFRACTIONr_bond_other_d0.0130.0171831
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.6952791
X-RAY DIFFRACTIONr_angle_other_deg2.1411.5984293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5665263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6623.204103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8481510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02444
X-RAY DIFFRACTIONr_rigid_bond_restr20.80433872
LS refinement shellResolution: 1.09→1.118 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 106 -
Rwork0.27 5945 -
all-6051 -
obs--88.56 %

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