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- PDB-5exc: Photoconverted red fluorescent protein DendRFP -

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Basic information

Entry
Database: PDB / ID: 5exc
TitlePhotoconverted red fluorescent protein DendRFP
Components(Green fluorescent protein) x 2
KeywordsFLUORESCENT PROTEIN / Photoswitchable fluorescent proteins / chromophore / beta-barrel / biomarker
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
Similarity search - Function
Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich ...Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesDendronephthya sp. SSAL-2002 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.
Authors: Pletneva, N.V. / Pletnev, S. / Pakhomov, A.A. / Chertkova, R.V. / Martynov, V.I. / Muslinkina, L. / Dauter, Z. / Pletnev, V.Z.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / entity / entity_poly / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_main_chain_plane.auth_asym_id / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_polymer_linkage.auth_asym_id_1 / _pdbx_validate_polymer_linkage.auth_asym_id_2 / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
aa: Green fluorescent protein
B: Green fluorescent protein
bb: Green fluorescent protein
C: Green fluorescent protein
cc: Green fluorescent protein
D: Green fluorescent protein
dd: Green fluorescent protein
E: Green fluorescent protein
ee: Green fluorescent protein
F: Green fluorescent protein
ff: Green fluorescent protein
G: Green fluorescent protein
gg: Green fluorescent protein
H: Green fluorescent protein
hh: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,37130
Polymers214,82716
Non-polymers54414
Water11,584643
1
A: Green fluorescent protein
aa: Green fluorescent protein
C: Green fluorescent protein
cc: Green fluorescent protein
E: Green fluorescent protein
ee: Green fluorescent protein
H: Green fluorescent protein
hh: Green fluorescent protein
hetero molecules


  • defined by author&software
  • 108 kDa, 8 polymers
Theoretical massNumber of molelcules
Total (without water)107,67616
Polymers107,4148
Non-polymers2628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27510 Å2
ΔGint-163 kcal/mol
Surface area34040 Å2
MethodPISA
2
F: Green fluorescent protein
ff: Green fluorescent protein
G: Green fluorescent protein
gg: Green fluorescent protein
hetero molecules

B: Green fluorescent protein
bb: Green fluorescent protein
D: Green fluorescent protein
dd: Green fluorescent protein
hetero molecules


  • defined by author&software
  • 108 kDa, 8 polymers
Theoretical massNumber of molelcules
Total (without water)107,69514
Polymers107,4148
Non-polymers2816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area28090 Å2
ΔGint-140 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.423, 69.521, 124.481
Angle α, β, γ (deg.)89.880, 89.940, 65.570
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Green fluorescent protein /


Mass: 6767.758 Da / Num. of mol.: 8 / Fragment: UNP residues 2-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendronephthya sp. SSAL-2002 (invertebrata)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8T6U0
#2: Protein
Green fluorescent protein /


Mass: 20085.619 Da / Num. of mol.: 8 / Fragment: UNP residues 62-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendronephthya sp. SSAL-2002 (invertebrata)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8T6U0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Mg formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.285
11H, H-K, -L20.253
11-H, -H+K, -L30.218
11-h,-k,l40.244
ReflectionResolution: 2.14→30 Å / Num. obs: 95569 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 0.885 / Net I/av σ(I): 21.071 / Net I/σ(I): 9.9 / Num. measured all: 348230
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.223.30.57695000.7470.3660.6840.82698.6
2.22-2.313.10.4494660.8020.2990.5341.32998.1
2.31-2.413.60.30494890.9080.1870.3580.80199.1
2.41-2.543.60.21795190.9450.1320.2540.82499.2
2.54-2.73.70.14795830.9740.0880.1720.87799.6
2.7-2.93.80.196250.9880.060.1160.93299.7
2.9-3.23.90.06795490.9930.0390.0780.92899.8
3.2-3.663.80.05196360.9950.030.0590.90699.8
3.66-4.613.80.03995970.9960.0230.0460.982100
4.61-303.90.02596050.9990.0140.0280.55399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.14→29.87 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 1744 1.9 %RANDOM
Rwork0.1945 ---
obs0.1961 88469 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.36 Å2 / Biso mean: 27.569 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å22.34 Å2-1.31 Å2
2---1.33 Å22.95 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.14→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14582 0 29 643 15254
Biso mean--21.85 22.44 -
Num. residues----1790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01915084
X-RAY DIFFRACTIONr_bond_other_d00.0213983
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.9720423
X-RAY DIFFRACTIONr_angle_other_deg3.815332305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.28451784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45524.409719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.319152543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1961563
X-RAY DIFFRACTIONr_chiral_restr0.1130.22100
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117085
X-RAY DIFFRACTIONr_gen_planes_other0.0120.023532
X-RAY DIFFRACTIONr_mcbond_it2.3832.8147170
X-RAY DIFFRACTIONr_mcbond_other2.3832.8137169
X-RAY DIFFRACTIONr_mcangle_it3.6824.2128945
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 54 -
Rwork0.262 3756 -
all-3810 -
obs--52.89 %

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