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- PDB-6grm: Structure of GFPmut2 crystallized at pH 6 and transferred to pH 9 -

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Basic information

Entry
Database: PDB / ID: 6grm
TitleStructure of GFPmut2 crystallized at pH 6 and transferred to pH 9
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta barrel / bioluminescence
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: 2.3 Å
AuthorsLolli, G. / Raboni, S. / Pasqualetto, E. / Campanini, B. / Mozzarelli, A. / Bettati, S. / Battistutta, R.
CitationJournal: J.Phys.Chem.B / Year: 2018
Title: Insight into GFPmut2 pH Dependence by Single Crystal Microspectrophotometry and X-ray Crystallography.
Authors: Lolli, G. / Raboni, S. / Pasqualetto, E. / Benoni, R. / Campanini, B. / Ronda, L. / Mozzarelli, A. / Bettati, S. / Battistutta, R.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)27,4341
Polymers27,4341
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-1 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.323, 59.686, 108.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 27433.920 Da / Num. of mol.: 1
Mutation: S65A, V68L, S72A: First six residues GSHIGP derive from the expression tag
Source method: isolated from a genetically manipulated source
Details: S65A, V68L, S72A: First six residues GSHIGP derive from the expression tag
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.84 Å3/Da / Density % sol: 33.33 %
Description: Crystal suffered from soaking in MPD 85% and change in pH from 6 to 9
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: MPD 45%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40.13 Å / Num. obs: 9288 / % possible obs: 97.9 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.053 / Rrim(I) all: 0.104 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.383.30.3319130.9120.2020.39199.1
8.91-40.132.90.0371810.9960.0240.04489.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.2.14data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q4A

1q4a


Resolution: 2.3→40.126 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.19
RfactorNum. reflection% reflection
Rfree0.2747 478 5.16 %
Rwork0.2257 --
obs0.2283 9269 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.72 Å2 / Biso mean: 34.4378 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 2.3→40.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 60 1873
Biso mean---32.78 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081867
X-RAY DIFFRACTIONf_angle_d1.222519
X-RAY DIFFRACTIONf_chiral_restr0.056268
X-RAY DIFFRACTIONf_plane_restr0.006328
X-RAY DIFFRACTIONf_dihedral_angle_d6.3011539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.63280.34761630.27132905306899
2.6328-3.31690.30251570.24692930308798
3.3169-40.13230.23661580.20162956311494

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