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- PDB-6go8: Structure of GFPmut2 crystallized at pH 6 -

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Basic information

Entry
Database: PDB / ID: 6go8
TitleStructure of GFPmut2 crystallized at pH 6
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: 1.648 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 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9075
Polymers27,4341
Non-polymers4734
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.504, 60.009, 112.497
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: Mutations: 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: 45% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.648→41.04 Å / Num. obs: 25496 / % possible obs: 93.5 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.648-1.682.50.21711830.940.1490.26689.3
9.03-41.043.50.0391680.9980.0240.04680.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1q4a


Resolution: 1.648→28.143 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.29
RfactorNum. reflection% reflection
Rfree0.174 1293 5.08 %
Rwork0.1554 --
obs0.1564 25456 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.51 Å2 / Biso mean: 13.3142 Å2 / Biso min: 3.01 Å2
Refinement stepCycle: final / Resolution: 1.648→28.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 32 312 2202
Biso mean--17.92 24.58 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061996
X-RAY DIFFRACTIONf_angle_d1.12716
X-RAY DIFFRACTIONf_chiral_restr0.062301
X-RAY DIFFRACTIONf_plane_restr0.006346
X-RAY DIFFRACTIONf_dihedral_angle_d6.0172052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6479-1.71390.24651440.20152663280793
1.7139-1.79180.20641470.17122734288197
1.7918-1.88630.22061310.16192731286295
1.8863-2.00440.18921130.15672721283494
2.0044-2.15920.16291350.1562721285694
2.1592-2.37630.17281510.15342642279393
2.3763-2.720.18041580.16092654281291
2.72-3.42590.16091520.14732622277490
3.4259-28.14710.14781620.14212675283787

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