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- PDB-5y01: Acid-tolerant monomeric GFP, Gamillus, non-fluorescence (OFF) state -

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Basic information

Entry
Database: PDB / ID: 5y01
TitleAcid-tolerant monomeric GFP, Gamillus, non-fluorescence (OFF) state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta barrel / gfp-like protein / cis-chromophore
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesOlindias (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNakashima, R. / Sakurai, K. / Shinoda, H. / Matsuda, T. / Nagai, T.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Acid-Tolerant Monomeric GFP from Olindias formosa.
Authors: Shinoda, H. / Ma, Y. / Nakashima, R. / Sakurai, K. / Matsuda, T. / Nagai, T.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7885
Polymers30,4081
Non-polymers3804
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.797, 161.797, 161.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Green fluorescent protein


Mass: 30408.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Olindias (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 5.8 Å3/Da / Density % sol: 78.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Ammonium phosphate, sodium citrate, sodium chloride, pH3.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.65→114 Å / Num. obs: 20148 / % possible obs: 98.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.763

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→80.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19582 983 4.9 %RANDOM
Rwork0.17254 ---
obs0.17366 19260 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.483 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.65→80.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 20 33 1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191875
X-RAY DIFFRACTIONr_bond_other_d00.021729
X-RAY DIFFRACTIONr_angle_refined_deg2.5681.9682541
X-RAY DIFFRACTIONr_angle_other_deg3.7233996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7675227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89924.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9215307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.651157
X-RAY DIFFRACTIONr_chiral_restr0.1310.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212085
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02431
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9143.977914
X-RAY DIFFRACTIONr_mcbond_other3.9083.975913
X-RAY DIFFRACTIONr_mcangle_it5.7655.9671139
X-RAY DIFFRACTIONr_mcangle_other5.7635.9711140
X-RAY DIFFRACTIONr_scbond_it6.2354.595960
X-RAY DIFFRACTIONr_scbond_other6.0414.567944
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.816.5691378
X-RAY DIFFRACTIONr_long_range_B_refined10.64431.8231969
X-RAY DIFFRACTIONr_long_range_B_other10.61831.8481965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.655→2.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 75 -
Rwork0.296 1383 -
obs--98.38 %

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