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- PDB-7av6: FAST in a domain-swapped dimer form -

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Basic information

Entry
Database: PDB / ID: 7av6
TitleFAST in a domain-swapped dimer form
ComponentsPhotoactive yellow protein
KeywordsFLUORESCENT PROTEIN / fluorescence / fluorogen / fluorogen-activating protein / fluorescent labelling / FAST
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBukhdruker, S. / Remeeva, A. / Ruchkin, D. / Gorbachev, D. / Povarova, N. / Mineev, K. / Goncharuk, S. / Baranov, M. / Mishin, A. / Borshchevskiy, V.
CitationJournal: Chem Sci / Year: 2021
Title: NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids.
Authors: Mineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Povarova, N.V. / Sokolov, A.I. / Baleeva, N.S. / Smirnov, A.Y. / Myasnyanko, I.N. / Ruchkin, D.A. / Bukhdruker, S. / Remeeva, A. / Mishin, ...Authors: Mineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Povarova, N.V. / Sokolov, A.I. / Baleeva, N.S. / Smirnov, A.Y. / Myasnyanko, I.N. / Ruchkin, D.A. / Bukhdruker, S. / Remeeva, A. / Mishin, A. / Borshchevskiy, V. / Gordeliy, V. / Arseniev, A.S. / Gorbachev, D.A. / Gavrikov, A.S. / Mishin, A.S. / Baranov, M.S.
History
DepositionNov 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3413
Polymers15,2491
Non-polymers922
Water37821
1
A: Photoactive yellow protein
hetero molecules

A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6826
Polymers30,4982
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4150 Å2
ΔGint-28 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.920, 45.920, 105.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Photoactive yellow protein / PYP / FAST


Mass: 15249.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAST / Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Plasmid: pET-24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16113
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.78 Å3/Da / Density % sol: 31.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.5→42.09 Å / Num. obs: 18549 / % possible obs: 98.5 % / Redundancy: 25.4 % / Biso Wilson estimate: 36.93 Å2 / CC1/2: 1 / Rpim(I) all: 0.007 / Net I/σ(I): 32.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.5-1.5423.90.712740.3250.72696.6
1.54-1.5826.11.212830.5850.48597.3
1.58-1.6227.11.812760.7230.34897.6
1.62-1.6826.92.712690.8420.24897.8
1.68-1.7426.24.312980.9340.16398.2
1.74-1.8125713000.9770.10198.1
1.81-1.8925.910.912980.990.06598.6
1.89-1.9926.918.113170.9970.03998.5
1.99-2.1126.42913190.9980.02498.9
2.11-2.2824.841.313200.9990.01699.1
2.28-2.525.456.413530.9990.01299.2
2.5-2.8725.873.4136210.00999.6
2.87-3.6123.189.5138610.00799.9
3.61-42.0923103.7149410.00699.9

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Processing

Software
NameVersionClassification
MxCuBE3data collection
XDS20200131data reduction
XSCALE20200131data scaling
MoRDa1.3.02phasing
ARP/wARP8model building
PHENIX1.18_3855refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ODV

1odv


Resolution: 1.5→42.08 Å / SU ML: 0.2024 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2372 927 5.01 %
Rwork0.2141 17591 -
obs0.2153 18518 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 6 21 762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053789
X-RAY DIFFRACTIONf_angle_d0.7361068
X-RAY DIFFRACTIONf_chiral_restr0.0717112
X-RAY DIFFRACTIONf_plane_restr0.0055141
X-RAY DIFFRACTIONf_dihedral_angle_d17.8633275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.37211280.34512419X-RAY DIFFRACTION96.59
1.58-1.680.32161270.28062410X-RAY DIFFRACTION97.65
1.68-1.810.28241310.2522473X-RAY DIFFRACTION98.15
1.81-1.990.26141300.23132482X-RAY DIFFRACTION98.53
1.99-2.280.24321320.22732502X-RAY DIFFRACTION98.95
2.28-2.870.27681350.24552574X-RAY DIFFRACTION99.41
2.87-42.080.21661440.1962731X-RAY DIFFRACTION99.9
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)
10.09733967781440.113861638535-0.002576501272150.127677430525-0.03107071737730.114725834974-0.292289094756-0.9393790249060.172714974508-0.1621247448420.4161140405070.01704465498740.443185766227-0.05443155388450.003580876604140.5846048231240.044370754351-0.04695008607410.543027258357-0.023753468690.6605993495223.7336487444730.523307856412.9871314983
20.06335753158350.119399755056-0.01927786992050.315832029415-0.4251359599490.7748769407680.048539714596-0.06126695900710.0659627350955-0.2298677162720.09391771688520.00738539850952-0.1405984694390.1152439561480.000582961021210.387606491834-0.006184178275920.02773517950260.272387513726-0.005821155182210.34836681145514.35639393234.613564224117.6371652156
30.0854473460101-0.179236411930.154009577880.543695981051-0.1622257233780.1507271259030.3816813800830.0274020974037-0.988940944283-0.313332818153-0.0477543090053-0.0851889490966-0.251854660273-0.2394168719810.007668648809090.3394467842090.0564098974940.06456970532050.4366880281550.07195187570980.4170361810519.9121593617838.785521510524.6697529503
41.590547475540.542771017803-0.5252649552280.97415888996-0.1253006546740.1621766518470.230134728571-0.396710493789-0.2643687851990.115495254896-0.052308485375-0.2156603514220.07260521791450.7719081898410.001054969338190.2738975582120.0141870554731-0.02456626964720.537744846170.04209310255430.35713314526921.024995356530.397998158639.6390682653
50.786172149748-0.3020658036750.0188926657680.1928208205130.0776494363280.1095586432320.055889883261-0.99234675478-1.320316197811.333836596040.208627981394-0.5672114972430.604662608573-0.165792403141-0.04723091004080.503294434598-0.0291747663426-0.05337804583880.6265492694550.2442386493950.55156655513614.912390131322.651903866746.5417180496
61.57381626853-1.350321241270.1836894972261.535955044920.06254933998560.262017252659-0.54292058995-1.199615406750.2118631205290.7649221096250.700724555017-0.2066992867350.13442956675-1.094277808010.06877754668630.533397835181-0.1824953404970.06837651291420.828691193150.1212601495520.34099789860813.976958654632.098554120550.6031328413
70.2548677543890.0268681269841-0.05334575125750.02924544627940.0321317091830.0530553395994-1.07153414250.271601275896-1.12806567494-0.107134510899-0.021359400449-0.154301974901-0.9798950616310.741123771681-0.00290568681040.681529601209-0.0272396867467-0.02855088001170.7105009712750.1050404338090.60952934599628.151775294745.460105105248.5129448002
80.472325725351-0.5252383086860.3238169175920.487902921902-0.2885422806860.421339640516-0.0962492120038-0.3447270591320.3532594276860.121487649563-0.1423073265220.2706720240680.402557501162-0.3952852302620.0008510641733290.371966399539-0.0133431443115-0.00635909511020.6706258108740.0292062130450.43734681940812.413047033235.032862309248.2524056989
90.860675849031-0.5303036258240.2029318464760.427605519912-0.4904653620651.00421674531-0.00612221781742-0.989476649236-0.381258876390.02482904224340.1190394735450.615880916474-0.0999033809439-0.7934545343240.0130164311810.308176290288-0.00338455851548-0.00215959231160.499206551820.003762421866480.4492109327627.512341650632.573645363942.8319617961
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 29 )25 - 291 - 5
22chain 'A' and (resid 30 through 44 )30 - 446 - 21
33chain 'A' and (resid 48 through 56 )48 - 5622 - 31
44chain 'A' and (resid 57 through 75 )57 - 7532 - 51
55chain 'A' and (resid 76 through 85 )76 - 8552 - 62
66chain 'A' and (resid 86 through 96 )86 - 9663 - 73
77chain 'A' and (resid 97 through 102 )97 - 10274 - 79
88chain 'A' and (resid 103 through 111 )103 - 11180 - 88
99chain 'A' and (resid 112 through 126 )112 - 12689 - 103

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