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- PDB-5dju: Crystal structure of LOV2 (C450A) domain in complex with Zdk3 -

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Basic information

Entry
Database: PDB / ID: 5dju
TitleCrystal structure of LOV2 (C450A) domain in complex with Zdk3
Components
  • Engineered protein, Zdk3 affibody
  • NPH1-2
KeywordsSIGNALING PROTEIN / Protein binding / Protein engineering / Photoswitch / Light-induced signal transduction / LOV2 / Affibody / Complex
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin FC, subunit C / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. ...Immunoglobulin FC, subunit C / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTarnawski, M. / Wang, H. / Yumerefendi, H. / Hahn, K.M. / Schlichting, I.
CitationJournal: Nat.Methods / Year: 2016
Title: LOVTRAP: an optogenetic system for photoinduced protein dissociation.
Authors: Wang, H. / Vilela, M. / Winkler, A. / Tarnawski, M. / Schlichting, I. / Yumerefendi, H. / Kuhlman, B. / Liu, R. / Danuser, G. / Hahn, K.M.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Jan 10, 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
B: Engineered protein, Zdk3 affibody
A: NPH1-2
D: Engineered protein, Zdk3 affibody
C: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00111
Polymers46,9114
Non-polymers1,0907
Water3,945219
1
B: Engineered protein, Zdk3 affibody
A: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0186
Polymers23,4552
Non-polymers5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-39 kcal/mol
Surface area10080 Å2
MethodPISA
2
D: Engineered protein, Zdk3 affibody
C: NPH1-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9835
Polymers23,4552
Non-polymers5273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-43 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.240, 74.500, 81.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Engineered protein, Zdk3 affibody


Mass: 6823.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein NPH1-2


Mass: 16631.729 Da / Num. of mol.: 2 / Fragment: UNP residues 404-546 / Mutation: C450A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O49004
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Mutation: C450A
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P / Source: (gene. exp.) Avena sativa (oats) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M citric acid pH 4.0, 1.0 M lithium chloride, 18% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26342 / % possible obs: 96.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.1 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WKQ and a homology model based on 1Q2N

2wkq

1q2n


Resolution: 2.1→44.252 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1318 5 %
Rwork0.2049 --
obs0.2075 26338 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 5 219 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083358
X-RAY DIFFRACTIONf_angle_d1.0734553
X-RAY DIFFRACTIONf_dihedral_angle_d15.0621269
X-RAY DIFFRACTIONf_chiral_restr0.046499
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.3441310.26622471X-RAY DIFFRACTION87
2.1841-2.28350.33031440.23832745X-RAY DIFFRACTION98
2.2835-2.40390.29561490.22982823X-RAY DIFFRACTION99
2.4039-2.55450.28281460.23072775X-RAY DIFFRACTION99
2.5545-2.75170.26491470.20942804X-RAY DIFFRACTION99
2.7517-3.02850.27981490.21272816X-RAY DIFFRACTION98
3.0285-3.46660.25171470.2022800X-RAY DIFFRACTION98
3.4666-4.36690.22031490.17782834X-RAY DIFFRACTION98
4.3669-44.26210.2321560.19162952X-RAY DIFFRACTION97
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)
13.39384.22782.65016.1411.86695.2823-0.00740.87180.4575-0.36780.20630.2827-0.10650.1907-0.31610.25680.07920.04910.3710.05210.2936-1.596313.8325-10.3308
22.3935-0.30920.05582.56690.59954.17930.0728-0.09310.40440.11540.0401-0.0497-0.14890.3518-0.07670.162-0.02360.04080.26670.0090.311-2.850514.68911.7736
32.3021-0.20460.424.12940.80652.30270.10270.0136-0.1456-0.11180.0067-0.15630.24260.2883-0.09630.20550.0115-0.03390.25180.02530.22423.2976-5.9501-8.0621
47.4405-5.8262-5.05175.01184.59824.5949-0.4517-0.1852-0.00850.87690.8062-0.35390.63830.5856-0.2550.33260.0115-0.1060.41310.0090.347214.3678-7.26760.2772
54.59664.2454.81543.92074.46566.0171-0.22060.15710.76550.14570.14020.5419-0.4252-0.04150.13220.21660.03560.03190.25870.00540.4394-16.7725-8.519-35.8718
60.3435-0.22140.372.737-0.10042.4767-0.08890.10180.04760.03750.1025-0.1302-0.0006-0.0216-0.01560.19260.0311-0.01290.2612-0.05660.369-15.7134-20.4839-36.8694
72.02610.46560.69721.3684-0.2153.790.0783-0.29480.01060.1140.02340.1511-0.1302-0.1193-0.10360.2153-0.01480.01840.2949-0.06960.347-22.3436-10.8187-16.2794
87.1218-4.5308-4.26145.30664.89425.3014-0.051-0.11090.39070.53820.26830.3620.842-0.8782-0.03540.3279-0.08220.06880.39350.06970.5408-33.736-18.7557-15.7311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 60 )
3X-RAY DIFFRACTION3chain 'B' and (resid 402 through 521 )
4X-RAY DIFFRACTION4chain 'B' and (resid 522 through 546 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 20 )
6X-RAY DIFFRACTION6chain 'C' and (resid 21 through 60 )
7X-RAY DIFFRACTION7chain 'D' and (resid 402 through 521 )
8X-RAY DIFFRACTION8chain 'D' and (resid 522 through 546 )

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