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- PDB-5t3i: cyan fluorescence protein soaked with selenourea for 5 min -

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Basic information

Entry
Database: PDB / ID: 5t3i
Titlecyan fluorescence protein soaked with selenourea for 5 min
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / cyan fluorescence protein / selenourea
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
PHOSPHATE ION / selenourea / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLuo, Z. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Rep / Year: 2016
Title: Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures.
Authors: Luo, Z.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,61515
Polymers26,9201
Non-polymers1,69414
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.116, 61.520, 69.559
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: 26920.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42212
#2: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH4N2Se
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16% (w/v) PEG 3350, 50 mM citric acid, and 50 mM bis-tris propane buffer pH 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30369 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→30.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.279 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1487 5 %RANDOM
Rwork0.134 ---
obs0.136 28216 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 57 154 2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191927
X-RAY DIFFRACTIONr_bond_other_d0.0020.021822
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9552594
X-RAY DIFFRACTIONr_angle_other_deg0.952.9634164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4225.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.065156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.022236
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02536
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_it2.4113.072920
X-RAY DIFFRACTIONr_mcbond_other2.3453.062919
X-RAY DIFFRACTIONr_mcangle_it2.8555.7611150
X-RAY DIFFRACTIONr_mcangle_other2.8685.7741151
X-RAY DIFFRACTIONr_scbond_it3.6543.8971007
X-RAY DIFFRACTIONr_scbond_other3.6553.8961004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2256.8811439
X-RAY DIFFRACTIONr_long_range_B_refined4.13414.0452083
X-RAY DIFFRACTIONr_long_range_B_other4.01313.7852035
X-RAY DIFFRACTIONr_rigid_bond_restr1.49633748
X-RAY DIFFRACTIONr_sphericity_free29.988565
X-RAY DIFFRACTIONr_sphericity_bonded8.5353805
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 90 -
Rwork0.198 1621 -
obs--77.14 %

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