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Entry
Database: PDB / ID: 1xmz
TitleCrystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata
Components
  • GFP-like non-fluorescent chromoprotein FP595 chain 1
  • GFP-like non-fluorescent chromoprotein FP595 chain 2
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN / CHROMOPHORE STRUCTURE / ASCP595
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / GFP-like non-fluorescent chromoprotein FP595
Similarity search - Component
Biological speciesAnemonia sulcata (snake-locks sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsQuillin, M.L. / Anstrom, D.M. / Shu, X. / O'Leary, S. / Kallio, K. / Chudakov, D.M. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 2005
Title: Kindling Fluorescent Protein from Anemonia sulcata: Dark-State Structure at 1.38 Resolution
Authors: Quillin, M.L. / Anstrom, D.M. / Shu, X. / O'Leary, S. / Kallio, K. / Chudakov, D.M. / Remington, S.J.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Natural Animal Coloration Can be Determined by a Nonfluorescent Green Fluorescent Protein Homolog
Authors: Lukyanov, K.A. / Fradkov, A.F. / Gurskaya, N.G. / Matz, M.V. / Labas, Y.A. / Savitsky, A.P. / Markelov, M.L. / Zaraisky, A.G. / Zhao, X. / Fang, Y. / Tan, W. / Lukyanov, S.A.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Alternative Cyclization in Gfp-Like Proteins Family. The Formation and Structure of the Chromophore of a Purple Chromoprotein from Anemonia Sulcata
Authors: Martynov, V.I. / Savitsky, A.P. / Martynova, N.Y. / Savitsky, P.A. / Lukyanov, K.A. / Lukyanov, S.A.
#3: Journal: BMC BIOCHEM. / Year: 2002
Title: Interconversion of Anthozoa Gfp-Like Fluorescent and Nonfluorescent Proteins by Mutagenesis
Authors: Bulina, M.E. / Chudakov, D.M. / Mudrik, N.N. / Lukyanov, K.A.
#4: Journal: J.Biol.Chem. / Year: 2002
Title: Chromophore Environment Provides Clue to "Kindling Fluorescent Protein" Riddle
Authors: Chudakov, D.M. / Foefanov, A.V. / Mudrik, N.N. / Lukyanov, S. / Lukyanov, K.A.
#5: Journal: NAT.BIOTECHNOL. / Year: 2003
Title: Kindling Fluorescent Proteins for Precise in Vivo Photolabeling
Authors: Chudakov, D.M. / Belousov, V.V. / Zaraisky, A.G. / Novoselov, V.V. / Staroverov, D.B. / Zorov, D.B. / Lukyanov, S. / Lukyanov, K.A.
#6: Journal: To be Published
Title: Synthesis and Properties of the Chromophore of Asulcp Chromoprotein from Anemonia Sulcata
Authors: Yampolsky, I.V. / Remington, S.J. / Potapov, V.K. / Lukyanov, K.A.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Feb 28, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_biol / 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_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.details / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_mod_residue.label_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_torsion.auth_asym_id / _struct_asym.entity_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Remark 999SEQUENCE RESIDUE MET 63, TYR 64 AND GLY 65 ARE MODIFIED TO FORM A CHROMOPHORE (CRK 65) IN BOTH CHAINS
Remark 400COMPOUND THE AMINO GROUP (NH2 240) FOLLOWING CYS 62 IS DERIVED FROM THE PEPTIDE NITROGEN OF MET 63

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein FP595 chain 1
C: GFP-like non-fluorescent chromoprotein FP595 chain 2
B: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,93311
Polymers54,3864
Non-polymers5477
Water8,341463
1
A: GFP-like non-fluorescent chromoprotein FP595 chain 1
C: GFP-like non-fluorescent chromoprotein FP595 chain 2
B: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules

A: GFP-like non-fluorescent chromoprotein FP595 chain 1
C: GFP-like non-fluorescent chromoprotein FP595 chain 2
B: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,86522
Polymers108,7718
Non-polymers1,09414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area34420 Å2
ΔGint-195 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 125.400, 92.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.188266, 0.002404, -0.982115), (0.004802, -0.999987, -0.001527), (-0.982106, -0.004428, -0.188275)
Vector: 99.384, 67.755, 120.493)

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Components

#1: Protein GFP-like non-fluorescent chromoprotein FP595 chain 1


Mass: 8065.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109 / References: UniProt: Q9GZ28
#2: Protein GFP-like non-fluorescent chromoprotein FP595 chain 2


Mass: 19127.678 Da / Num. of mol.: 2 / Mutation: A143G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109 / References: UniProt: Q9GZ28
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 26% PEG 1550, 0.14 M SODIUM CITRATE, 0.1 M TRIS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 89428 / Num. obs: 89428 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 49.1
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 8.4 / Num. unique all: 8895 / % possible all: 97.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G7K

1g7k


Resolution: 1.38→50 Å / Num. parameters: 38699 / Num. restraintsaints: 48588 / Isotropic thermal model: INDIVIDUAL ANISOTROPIC B-FACTORS / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 4307 5.1 %SHELLS
Rwork0.1393 ---
all0.1404 89373 --
obs0.1404 89373 96.5 %-
Solvent computationSolvent model: A solvent model based on Moews & Kretsinger, 1975 was applied during refinement.
Refine analyzeNum. disordered residues: 46 / Occupancy sum hydrogen: 3322 / Occupancy sum non hydrogen: 4108
Refinement stepCycle: LAST / Resolution: 1.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 30 463 4108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0327
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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