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- PDB-4kex: Crystal structure analysis of a single amino acid deletion mutati... -

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Basic information

Entry
Database: PDB / ID: 4kex
TitleCrystal structure analysis of a single amino acid deletion mutation in EGFP
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta barrel / chromophore cyclisation / single amino acid deletion mutation
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: 1.6 Å
AuthorsArpino, J.A.J. / Rizkallah, P.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein.
Authors: Arpino, J.A. / Rizkallah, P.J. / Jones, D.D.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 25, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: 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 / 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 1.4Dec 6, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)26,8851
Polymers26,8851
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.450, 63.140, 65.700
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: 26885.365 Da / Num. of mol.: 1 / Mutation: F64L, S65T, A227delta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pNOM-XP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4
Details: 0.1 M MMT Buffer (Malic acid, MES and Tris), 25% (w/v) PEG 1500, pH 4.0, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→51.45 Å / Num. obs: 28209 / % possible obs: 98.1 % / Redundancy: 7.9 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.75 Å45.52 Å
Translation5.75 Å45.52 Å

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Processing

Software
NameVersionClassificationNB
SCALA0.1.16data scaling
PHASER2.5.1phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EUL

4eul


Resolution: 1.6→45.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.1769 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8629 / SU B: 3.73 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1016 / SU Rfree: 0.0964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1417 5 %RANDOM
Rwork0.1823 ---
obs0.1837 28165 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.95 Å2 / Biso mean: 17.9795 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 0 208 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191956
X-RAY DIFFRACTIONr_bond_other_d0.0060.021811
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.9612663
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0014180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9425244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72225.05297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.534157
X-RAY DIFFRACTIONr_chiral_restr0.1390.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212276
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02455
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 106 -
Rwork0.213 1924 -
all-2030 -
obs--97.08 %
Refinement TLS params.Method: refined / Origin x: 25.8219 Å / Origin y: -2.5613 Å / Origin z: -2.5733 Å
111213212223313233
T0.0036 Å20 Å20.0021 Å2-0.0085 Å20.0044 Å2--0.0045 Å2
L0.2636 °20.0778 °2-0.0006 °2-0.3486 °20.012 °2--0.2698 °2
S-0.0008 Å °0.0255 Å °0.0217 Å °0.0022 Å °0.0175 Å °0.0212 Å °-0.03 Å °-0.0042 Å °-0.0167 Å °

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