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- PDB-2fl1: Crystal structure of red fluorescent protein from Zoanthus, zRFP5... -

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Basic information

Entry
Database: PDB / ID: 2fl1
TitleCrystal structure of red fluorescent protein from Zoanthus, zRFP574, at 2.4A resolution
ComponentsRed fluorescent protein zoanRFP
KeywordsFLUORESCENT PROTEIN / Red fluorescent protein / button polyp / Zoanthus sp. / chromophore / beta-can fold / beta barrel / tightly packed tetramer / intersubunit interface / fluorescent marker / emission maximum 574nm / zRFP574
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein zoanRFP
Function and homology information
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPletnev, V. / Pletneva, N. / Martynov, V. / Tikhonova, T. / Popov, B. / Pletnev, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of a red fluorescent protein from Zoanthus, zRFP574, reveals a novel chromophore
Authors: Pletneva, N. / Pletnev, S. / Tikhonova, T. / Popov, V. / Martynov, V. / Pletnev, V.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Chromophore (XYG 66) is formed autocatalytically from Asp-Tyr-Gly (according to nucleotide ...SEQUENCE Chromophore (XYG 66) is formed autocatalytically from Asp-Tyr-Gly (according to nucleotide sequence) after decarboxylation of Asp and other deprotonation processes.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red fluorescent protein zoanRFP
B: Red fluorescent protein zoanRFP
C: Red fluorescent protein zoanRFP
D: Red fluorescent protein zoanRFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,77113
Polymers103,9064
Non-polymers8659
Water7,422412
1
A: Red fluorescent protein zoanRFP
D: Red fluorescent protein zoanRFP
hetero molecules

A: Red fluorescent protein zoanRFP
D: Red fluorescent protein zoanRFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,67412
Polymers103,9064
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
2
B: Red fluorescent protein zoanRFP
C: Red fluorescent protein zoanRFP
hetero molecules

B: Red fluorescent protein zoanRFP
C: Red fluorescent protein zoanRFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,86714
Polymers103,9064
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)114.927, 146.799, 122.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTwo dimers in assymetric unit. The tightly packed tetramers generated by crystallographic symmetry operations (-x-1, y, -z-1/2) and (-z, y, -z-1/2) .

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Components

#1: Protein
Red fluorescent protein zoanRFP


Mass: 25976.486 Da / Num. of mol.: 4 / Mutation: K5A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109DE3 / References: UniProt: Q8T4U4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 1.5M ammonium sulphate, 0.2M K/Na Tartrate, 0.1M Na Citrate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 40898 / Num. obs: 40878 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4051 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CCP4model building
CNS1.1refinement
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XA9

1xa9


Resolution: 2.4→30 Å / Isotropic thermal model: Isotropic / Cross valid method: Rfree throughout / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cross validated maximum likelihood, simulated annealing refinement
RfactorNum. reflectionSelection details
Rfree0.249 2048 random 5% reflections
Rwork0.203 --
all-40898 -
obs-40878 -
Displacement parametersBiso mean: 28.8 Å2
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.27 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 45 412 7753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_dihedral_angle_d25.9

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