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- PDB-2qt2: Cyclized-Dehydrated Intermediate of GFP Variant Q183E in Chromoph... -

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Basic information

Entry
Database: PDB / ID: 2qt2
TitleCyclized-Dehydrated Intermediate of GFP Variant Q183E in Chromophore Maturation
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / chromophore maturation / cyclized / dehydrated intermediate / Chromophore / 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 / Resolution: 1.31 Å
AuthorsWood, T.I. / Barondeau, D.P. / Hitomi, C. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: To be Published
Title: Kinetically Isolated Reaction Intermediates Provide Structural Characterization of the Green Fluorescence Protein Fluorophore Biosynthesis Pathway
Authors: Wood, T.I. / Barondeau, D.P. / Hitomi, C. / Tainer, J.A. / Getzoff, E.D.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: 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 ...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 1.3Aug 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9554
Polymers26,7691
Non-polymers1863
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.753, 62.143, 69.638
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: 26769.076 Da / Num. of mol.: 1 / Mutation: F64L, F99S, M153T, V163A, Q183E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pTIW188 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3, pRIL / References: UniProt: P42212
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg4000, Magnesium chloride, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. all: 52987 / Num. obs: 52987 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.59 / Redundancy: 4.47 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.041
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 3.31 % / Mean I/σ(I) obs: 3.59 / Num. unique all: 4570 / Rsym value: 0.35 / % possible all: 86.4

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ema

1ema


Resolution: 1.31→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.59
RfactorNum. reflectionSelection details
Rfree0.189 2644 random
Rwork0.133 --
all0.189 50260 -
obs0.189 50260 -
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 12 435 2310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_bond_d0.013
LS refinement shellResolution: 1.31→1.39 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.381 388 -
Rwork0.392 --
obs-7307 82.8 %

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