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- PDB-4q7r: Crystal structure of large Stokes shift fluorescent protein LSSmOrange -

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Basic information

Entry
Database: PDB / ID: 4q7r
TitleCrystal structure of large Stokes shift fluorescent protein LSSmOrange
ComponentsLSSmOrange
KeywordsFLUORESCENT PROTEIN / beta-barrel / large Stokes shift fluorescent protein / chromophore
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
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
ACETATE ION / mOrange
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPletnev, S. / Dauter, Z.
CitationJournal: Plos One / Year: 2014
Title: Orange Fluorescent Proteins: Structural Studies of LSSmOrange, PSmOrange and PSmOrange2.
Authors: Pletnev, S. / Shcherbakova, D.M. / Subach, O.M. / Pletneva, N.V. / Malashkevich, V.N. / Almo, S.C. / Dauter, Z. / Verkhusha, V.V.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LSSmOrange
B: LSSmOrange
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,88528
Polymers56,2412
Non-polymers1,64326
Water5,423301
1
A: LSSmOrange
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12917
Polymers28,1211
Non-polymers1,00816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LSSmOrange
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,75611
Polymers28,1211
Non-polymers63510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.436, 107.364, 56.602
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LSSmOrange


Mass: 28120.748 Da / Num. of mol.: 2 / Mutation: R17H, V44A, F83L, W143M, I161D, M163L, G196D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D0VWW2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES PHE65, GLY66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE.

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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: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M zinc acetate, 0.1 M acetate buffer, 20% PEG1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→55.335 Å / Num. obs: 84546 / % possible obs: 98.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.056 / Χ2: 1.014 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.454.10.62883450.76197.1
1.45-1.514.20.45582980.766197.6
1.51-1.584.20.30283910.783197.9
1.58-1.664.20.21283610.833198.2
1.66-1.764.20.14684600.864198.5
1.76-1.94.30.09784470.983198.8
1.9-2.094.30.06784971.115199.1
2.09-2.394.30.06885121.103199.4
2.39-3.024.30.05985811.209199.8
3.02-304.20.03486541.681199.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5O

2h5o


Resolution: 1.4→55.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1763 / WRfactor Rwork: 0.153 / FOM work R set: 0.9086 / SU B: 1.922 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0633 / SU Rfree: 0.0555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 1687 2 %RANDOM
Rwork0.1473 ---
obs0.1479 84451 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.67 Å2 / Biso mean: 18.796 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.07 Å2
2---0.1 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→55.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 53 301 3903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193955
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9865347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92224.372183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93915727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5291521
X-RAY DIFFRACTIONr_chiral_restr0.1590.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213105
X-RAY DIFFRACTIONr_rigid_bond_restr5.9133955
X-RAY DIFFRACTIONr_sphericity_free19.134597
X-RAY DIFFRACTIONr_sphericity_bonded9.68654069
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 125 -
Rwork0.21 5917 -
all-6042 -
obs--96.26 %

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