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- PDB-4h48: 1.45 angstrom CyPet Structure at pH7.0 -

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Basic information

Entry
Database: PDB / ID: 4h48
Title1.45 angstrom CyPet Structure at pH7.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Beta Barrel / 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: 1.45 Å
AuthorsHu, X.-J. / Liu, R.
CitationJournal: To be Published
Title: Structure insight of the fluorescent state of CyPet
Authors: Liu, R. / Zhou, Y.-B. / Ding, Y. / Hu, X.-J.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0092
Polymers26,8871
Non-polymers1221
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.880, 62.920, 70.210
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: 26887.344 Da / Num. of mol.: 1 / Mutation: T9G, V11I, D19E, A87V, I167A, E172T, L194I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) RESIDUES SER 65, TYR 66 HAVE BEEN MUTATED TO THR 65, TRP 66. RESIDUES THR 65, TRP 66 AND GLY 67 ...(1) RESIDUES SER 65, TYR 66 HAVE BEEN MUTATED TO THR 65, TRP 66. RESIDUES THR 65, TRP 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CRF 66. (2) RESIDUES LEU 64, ILE 146, THR 153, ALA 163 ARE THE NEUTRAL MUTATIONS.

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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: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.45→35.1 Å / Num. all: 40574 / Num. obs: 39804 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.45→1.53 Å / Rmerge(I) obs: 0.291 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I19

3i19


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.144 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.067 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1987 5 %RANDOM
Rwork0.17838 ---
obs0.18004 37772 97.79 %-
all-38625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0 Å2
2---1.08 Å2-0 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 8 160 1987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191900
X-RAY DIFFRACTIONr_bond_other_d0.0010.021784
X-RAY DIFFRACTIONr_angle_refined_deg2.61.9712572
X-RAY DIFFRACTIONr_angle_other_deg1.02534120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62425.16591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11615323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.688156
X-RAY DIFFRACTIONr_chiral_restr0.150.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212154
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02438
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 126 -
Rwork0.27 2792 -
obs--98.95 %

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