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- PDB-4nws: Crystal structure of PSLssmKate, a photoswitchable LSSmKate variant -

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Basic information

Entry
Database: PDB / ID: 4nws
TitleCrystal structure of PSLssmKate, a photoswitchable LSSmKate variant
Componentsfluorescent protein
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Fluorescent protein FP480
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMalashkevich, V.N. / Piatkevich, K. / Almo, S.C. / Verkhusha, V.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of PSLssmKate, a photoswitchable LSSmKate variant
Authors: Malashkevich, V.N. / Piatkevich, K. / Almo, S.C. / Verkhusha, V.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fluorescent protein
B: fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,2492
Polymers55,2492
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-17 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.032, 99.032, 106.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein fluorescent protein


Mass: 27624.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PBAD/HIS-B / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D0VX33*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M citric acid, pH 3.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12943 / % possible obs: 91.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.078 / Χ2: 0.983 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.751.50.3362500.71134.8
2.75-2.81.80.2733440.641150.5
2.8-2.852.20.2575010.598169.1
2.85-2.912.90.2465920.715185.3
2.91-2.973.80.256530.629194.8
2.97-3.044.80.2356840.783197.3
3.04-3.125.50.1917070.79199.4
3.12-3.25.70.1626790.86199.4
3.2-3.360.1267310.9531100
3.3-3.460.1076941.051100
3.4-3.5260.0917091.0581100
3.52-3.6660.0877291.1351100
3.66-3.8360.0776881.261100
3.83-4.0360.0756961.0791100
4.03-4.295.90.0657061.209199.9
4.29-4.625.80.0627060.9051100
4.62-5.085.90.0657020.8391100
5.08-5.815.80.0677300.9911100
5.81-7.325.80.0587121.0041100
7.32-505.70.0377301.1161100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NT9

3nt9


Resolution: 2.7→36.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2492 / WRfactor Rwork: 0.1735 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8362 / SU B: 23.237 / SU ML: 0.239 / SU R Cruickshank DPI: 0.058 / SU Rfree: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 642 5 %RANDOM
Rwork0.1786 ---
obs0.1821 12906 91.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.08 Å2 / Biso mean: 44.879 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.78 Å20 Å20 Å2
2--6.78 Å20 Å2
3----13.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 0 97 3669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193656
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9764930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08224.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8731518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212760
X-RAY DIFFRACTIONr_mcbond_it1.6177.3471782
X-RAY DIFFRACTIONr_mcangle_it2.8662220
X-RAY DIFFRACTIONr_scbond_it2.3327.8491874
LS refinement shellResolution: 2.703→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 14 -
Rwork0.242 373 -
all-387 -
obs--37.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8645-0.10540.49411.1554-0.33812.34740.02070.0657-0.1186-0.03590.0688-0.06610.13440.0262-0.08950.02090.00030.02530.0102-0.01330.08454.672228.0202-22.4034
21.2426-0.08140.84090.916-0.37861.7855-0.1683-0.3175-0.07380.03720.20190.0809-0.2849-0.5387-0.03360.04760.09060.00880.23650.06540.0422-20.86141.8743-31.2397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 228
2X-RAY DIFFRACTION2B3 - 228

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