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- PDB-4zfs: Phototoxic Fluorescent Protein KillerOrange -

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Basic information

Entry
Database: PDB / ID: 4zfs
TitlePhototoxic Fluorescent Protein KillerOrange
ComponentsKillerOrange
KeywordsFLUORESCENT PROTEIN / genetically encoded photosensitizer / chromophore-assisted light inactivation
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
Biological speciesHydrozoa (hydrozoans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsPletneva, N.V. / Pletnev, V.Z. / Pletnev, S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00281 Russian Federation
CitationJournal: Plos One / Year: 2015
Title: Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore.
Authors: Pletneva, N.V. / Pletnev, V.Z. / Sarkisyan, K.S. / Gorbachev, D.A. / Egorov, E.S. / Mishin, A.S. / Lukyanov, K.A. / Dauter, Z. / Pletnev, S.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
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 / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KillerOrange
B: KillerOrange
C: KillerOrange
D: KillerOrange
E: KillerOrange


Theoretical massNumber of molelcules
Total (without water)138,1315
Polymers138,1315
Non-polymers00
Water15,529862
1
A: KillerOrange
D: KillerOrange


Theoretical massNumber of molelcules
Total (without water)55,2522
Polymers55,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-25 kcal/mol
Surface area19570 Å2
MethodPISA
2
B: KillerOrange
E: KillerOrange


Theoretical massNumber of molelcules
Total (without water)55,2522
Polymers55,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-26 kcal/mol
Surface area19890 Å2
MethodPISA
3
C: KillerOrange

C: KillerOrange


Theoretical massNumber of molelcules
Total (without water)55,2522
Polymers55,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area2850 Å2
ΔGint-27 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.930, 202.064, 116.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-455-

HOH

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Components

#1: Protein
KillerOrange


Mass: 27626.117 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrozoa (hydrozoans) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2TCH5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.02M Na acetate, 1% gamma-PGA (Na+ form, LM), 3% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 101443 / % possible obs: 100 % / Redundancy: 17 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.03 / Rrim(I) all: 0.127 / Χ2: 1.157 / Net I/av σ(I): 20.526 / Net I/σ(I): 8 / Num. measured all: 1724142
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2-2.0714.70.435100250.9880.1130.450.915
2.07-2.1515.60.389100550.9910.0990.4020.954
2.15-2.2515.70.384100960.9820.10.3981.14
2.25-2.3716.70.302100580.9940.0750.3111.338
2.37-2.5217.90.241100610.9950.0580.2481.217
2.52-2.7118.20.187101220.9970.0450.1931.277
2.71-2.9918.30.15101400.9980.0360.1541.256
2.99-3.4218.20.121101500.9980.0290.1241.266
3.42-4.3117.10.1102380.9980.0240.1031.14
4.31-3017.40.081104980.9980.020.0830.999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZBL

4zbl


Resolution: 2.01→29.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2468 / WRfactor Rwork: 0.2007 / FOM work R set: 0.729 / SU B: 4.643 / SU ML: 0.121 / SU R Cruickshank DPI: 0.0341 / SU Rfree: 0.0324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 994 1 %RANDOM
Rwork0.1919 ---
obs0.1923 100074 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.41 Å2 / Biso mean: 45.771 Å2 / Biso min: 22.54 Å2
Baniso -1Baniso -2Baniso -3
1-86.43 Å20 Å20 Å2
2---52.31 Å2-0 Å2
3----34.11 Å2
Refinement stepCycle: final / Resolution: 2.01→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 0 862 9922
Biso mean---57.4 -
Num. residues----1152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199480
X-RAY DIFFRACTIONr_bond_other_d0.0010.028626
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9512879
X-RAY DIFFRACTIONr_angle_other_deg0.966319922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16251171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67923.64445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68151504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5971558
X-RAY DIFFRACTIONr_chiral_restr0.1420.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110882
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022274
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 62 -
Rwork0.344 7102 -
all-7164 -
obs--96.38 %

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