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- PDB-2a54: fluorescent protein asFP595, A143S, on-state, 1min irradiation -

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Basic information

Entry
Database: PDB / ID: 2a54
Titlefluorescent protein asFP595, A143S, on-state, 1min irradiation
Components
  • GFP-like non-fluorescent chromoprotein FP595 chain 1
  • GFP-like non-fluorescent chromoprotein FP595 chain 2
KeywordsLUMINESCENT PROTEIN / asCP / fluorescent protein / chromoprotein / photochromic protein / reversible photoswitch
Function / homology
Function and homology information


Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GFP-like non-fluorescent chromoprotein FP595
Similarity search - Component
Biological speciesAnemonia sulcata (snake-locks sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAndresen, M. / Wahl, M.C. / Stiel, A.C. / Graeter, F. / Schaefer, L. / Trowitzsch, S. / Weber, G. / Eggeling, C. / Grubmueller, H. / Hell, S.W. / Jakobs, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure and mechanism of the reversible photoswitch of a fluorescent protein
Authors: Andresen, M. / Wahl, M.C. / Stiel, A.C. / Graeter, F. / Schaefer, L. / Trowitzsch, S. / Weber, G. / Eggeling, C. / Grubmueller, H. / Hell, S.W. / Jakobs, S.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein FP595 chain 1
B: GFP-like non-fluorescent chromoprotein FP595 chain 2
C: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5175
Polymers54,4824
Non-polymers351
Water10,341574
1
A: GFP-like non-fluorescent chromoprotein FP595 chain 1
B: GFP-like non-fluorescent chromoprotein FP595 chain 2
C: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules

A: GFP-like non-fluorescent chromoprotein FP595 chain 1
B: GFP-like non-fluorescent chromoprotein FP595 chain 2
C: GFP-like non-fluorescent chromoprotein FP595 chain 1
D: GFP-like non-fluorescent chromoprotein FP595 chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,03510
Polymers108,9648
Non-polymers712
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area30860 Å2
ΔGint-184 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.539, 125.946, 93.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

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Components

#1: Protein GFP-like non-fluorescent chromoprotein FP595 chain 1 / asFP595


Mass: 8067.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus / References: UniProt: Q9GZ28
#2: Protein GFP-like non-fluorescent chromoprotein FP595 chain 2 / asFP595


Mass: 19173.727 Da / Num. of mol.: 2 / Mutation: A143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus / References: UniProt: Q9GZ28
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES MET 63, TYR 64 AND GLY 65 AUTOCATALYTICALLY FORM THE CHROMOPHORE NRQ LABELLED AS RESIDUE ...RESIDUES MET 63, TYR 64 AND GLY 65 AUTOCATALYTICALLY FORM THE CHROMOPHORE NRQ LABELLED AS RESIDUE 65 IN THE COORDINATES.

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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: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG 3350, NaCl, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 2005
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 80400 / Num. obs: 77265 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.5 Å / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.305 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 3882 5 %RANDOM
Rwork0.17586 ---
all0.17707 76336 --
obs0.17707 73359 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 1 574 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223838
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9785196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20123.865163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70715623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8861514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022960
X-RAY DIFFRACTIONr_nbd_refined0.2130.21730
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2426
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.238
X-RAY DIFFRACTIONr_mcbond_it1.69422410
X-RAY DIFFRACTIONr_mcangle_it2.2933739
X-RAY DIFFRACTIONr_scbond_it2.13821686
X-RAY DIFFRACTIONr_scangle_it3.05231449
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 300 -
Rwork0.22 5176 -
obs--93.77 %
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)
10.2192-0.0826-0.01060.8601-0.0770.3635-0.02030.0570.0577-0.06670.09570.1663-0.029-0.0583-0.0754-0.0336-0.0105-0.0166-0.00750.0455-0.009726.12944.89214.746
20.6286-0.09380.17571.0293-0.06170.40010.00910.0777-0.1595-0.14560.04070.1560.0633-0.0193-0.0498-0.0197-0.0275-0.0362-0.0346-0.01330.001527.67613.63913.003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 6210 - 73
2X-RAY DIFFRACTION1BB65 - 2321 - 168
3X-RAY DIFFRACTION2CC4 - 6215 - 73
4X-RAY DIFFRACTION2DD65 - 2321 - 168

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