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- PDB-1c4f: GREEN FLUORESCENT PROTEIN S65T AT PH 4.6 -

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Basic information

Entry
Database: PDB / ID: 1c4f
TitleGREEN FLUORESCENT PROTEIN S65T AT PH 4.6
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / GREEN FLUORESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG / PH TITRATION / SIGNALING PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsElsliger, M.A. / Wachter, R.M. / Kallio, K. / Hanson, G.T. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1999
Title: Structural and spectral response of green fluorescent protein variants to changes in pH.
Authors: Elsliger, M.A. / Wachter, R.M. / Hanson, G.T. / Kallio, K. / Remington, S.J.
#1: Journal: Structure / Year: 1998
Title: Structural Basis of Spectral Shifts in the Yellow-Emission Variants of Green Fluorescent Protein
Authors: Wachter, R.M. / Elsliger, M.A. / Kallio, K. / Hanson, G.T. / Remington, S.J.
#2: Journal: Biochemistry / Year: 1997
Title: Crystal Structure and Photodynamic Behavior of the Blue Emission Variant Y66H/ Y145F of Green Fluorescent Protein
Authors: Wachter, R.M. / King, B.A. / Heim, R. / Kallio, K. / Tsien, R.Y. / Boxer, S.G. / Remington, S.J.
#3: Journal: Science / Year: 1996
Title: Crystal Structure of the Aequorea Victoria Green Fluorescent Protein
Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionAug 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.8Feb 5, 2025Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9451
Polymers26,9451
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.934, 62.898, 69.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein GREEN FLUORESCENT PROTEIN


Mass: 26945.383 Da / Num. of mol.: 1
Mutation: 65 - 67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R SUBSTITUTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 1-3 NOT SEEN IN DENSITY MAPS RESIDUES 230-238 NOT SEEN IN DENSITY MAPS THE FLUOROPHORE ...RESIDUES 1-3 NOT SEEN IN DENSITY MAPS RESIDUES 230-238 NOT SEEN IN DENSITY MAPS THE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE BETWEEN THE NITROGEN OF GLY 67 AND THE CARBONYL CARBON OF THR 65. THE CARBONYL OXYGEN OF THR 65 LEAVES AS WATER, AND IS NOT PRESENT IN THE MODEL. A SUBSEQUENT OXIDATION OF THE CA - CB BOND OF TYR 66 LINKS THE CONJUGATED SYSTEM OF THE TYROSINE RING TO THAT OF THE FORMED BACKBONE IMIDAZOLIDINONE. RESIDUES 65, 66, AND 67 ARE NOT PRESENT IN THE ENTRY AND ARE INSTEAD REPLACED WITH CRO 66.

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 10-13% PEG 3400, 100MM SODIUM ACETATE AND 100 MM AMMONIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 mMTris-HCl1drop
310-13 %PEG34001reservoir
4100 mMsodium acetate1reservoir
5100 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→24.3 Å / Num. obs: 14685 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
CCP4model building
PROTEINmodel building
TNT5Frefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
PROTEINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA

1ema


Resolution: 2.25→24 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.193 --
obs-14685 96 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 140 Å2 / ksol: 0.822 e/Å3
Refinement stepCycle: LAST / Resolution: 2.25→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 62 1777
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01118550.6
X-RAY DIFFRACTIONt_angle_deg2.19725011.1
X-RAY DIFFRACTIONt_dihedral_angle_d20.19710820
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004522
X-RAY DIFFRACTIONt_gen_planes0.0092655
X-RAY DIFFRACTIONt_it4.13518411
X-RAY DIFFRACTIONt_nbd0.0191910
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.1970
X-RAY DIFFRACTIONt_plane_restr0.0095

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