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- PDB-3dqd: Structure of the Yellow Fluorescent Protein Citrine Frozen at 125... -

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Basic information

Entry
Database: PDB / ID: 3dqd
TitleStructure of the Yellow Fluorescent Protein Citrine Frozen at 1250 Atmospheres Number 2: Structure 12 in a Series of 26 High Pressure Structures
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / Yellow Fluorescent Protein / beta barrel / chromophore / fluorescent protein / high pressure / Luminescence / Photoprotein
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 / molecular replacement / Resolution: 1.4 Å
AuthorsBarstow, B. / Kim, C.U.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.
Authors: Barstow, B. / Ando, N. / Kim, C.U. / Gruner, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: High-pressure cooling of protein crystals without cryoprotectants.
Authors: Kim, C.U. / Kapfer, R. / Gruner, S.M.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,3941
Polymers27,3941
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.193, 62.977, 71.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 27393.916 Da / Num. of mol.: 1 / Mutation: S65G, V68L, Q69M, S72A, T203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CR2 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: 2.09 Å3/Da / Density % sol: 41.23 %
Description: Crystal structure of the Yellow Fluorescent Protein Citrine frozen at 1250 atmospheres. Structure 12 of 26 in a series of high pressure structures. Crystal was high pressure cryo-cooled ...Description: Crystal structure of the Yellow Fluorescent Protein Citrine frozen at 1250 atmospheres. Structure 12 of 26 in a series of high pressure structures. Crystal was high pressure cryo-cooled at 1250 atmospheres in helium gas. Crystal temperature was maintained below 100 K prior to data collection at ambient pressure and 100 K. High pressure cryo-cooling procedure is described in secondary citation 1 (Kim et al., Acta Cryst. D61:881-890). Structure referred to as citrine1250_2 in primary citation (Barstow et al.).
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, ...Details: Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2005
RadiationMonochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→39.72 Å / Num. obs: 27256 / % possible obs: 59.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 10.3
Reflection shellHighest resolution: 1.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.303 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å35.56 Å
Translation1.98 Å35.56 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
DPSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUY WITH RESIDUE 80 MUTATED TO GLUTAMINE

1huy


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.711 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. This structure is refined slightly differently from the corresponding structure used for analysis in the primary citation (Barstow et ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. This structure is refined slightly differently from the corresponding structure used for analysis in the primary citation (Barstow et al.). However, analysis of the deformation motion of the chromophore under pressure in this sequence of deposited structures produces an identical deformation trend. For copies of the structures as used in the analysis in the primary citation please contact the authors.
RfactorNum. reflection% reflectionSelection details
Rfree0.28004 1355 5 %RANDOM
Rwork0.21271 ---
obs0.21605 25884 59.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 260 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2511.9662559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2125228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62925.10992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.143156
X-RAY DIFFRACTIONr_chiral_restr0.150.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.2974
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21218
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8121.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11621841
X-RAY DIFFRACTIONr_scbond_it3.8563816
X-RAY DIFFRACTIONr_scangle_it5.5924.5718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.789 1 -
Rwork0.552 1 -
obs--0.06 %

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