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- PDB-5djt: Crystal structure of LOV2 (C450A) domain in complex with Zdk2 -

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Basic information

Entry
Database: PDB / ID: 5djt
TitleCrystal structure of LOV2 (C450A) domain in complex with Zdk2
Components
  • Engineered protein, Zdk2 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 / metal ion binding
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
COPPER (II) ION / FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesAvena sativa (oats)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
A: NPH1-2
B: Engineered protein, Zdk2 affibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8625
Polymers23,3062
Non-polymers5553
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-39 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.140, 110.140, 37.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NPH1-2


Mass: 16631.729 Da / Num. of mol.: 1 / 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
#2: Protein Engineered protein, Zdk2 affibody


Mass: 6674.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 279 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 32% (w/v) PEG 4000 and 0.1 M copper(II) chloride as an additive

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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: 1.4→50 Å / Num. obs: 44465 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7

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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 2KZJ

2wkq

2kzj


Resolution: 1.4→35.507 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 2223 5 %
Rwork0.1458 --
obs0.1471 44463 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→35.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 33 276 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111716
X-RAY DIFFRACTIONf_angle_d1.3432332
X-RAY DIFFRACTIONf_dihedral_angle_d15.917660
X-RAY DIFFRACTIONf_chiral_restr0.093259
X-RAY DIFFRACTIONf_plane_restr0.007304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.43050.28281390.29522661X-RAY DIFFRACTION100
1.4305-1.46380.24921360.19552573X-RAY DIFFRACTION99
1.4638-1.50040.21141390.14452637X-RAY DIFFRACTION100
1.5004-1.54090.15731370.12242601X-RAY DIFFRACTION100
1.5409-1.58630.15511370.11872618X-RAY DIFFRACTION100
1.5863-1.63750.16261400.12072660X-RAY DIFFRACTION100
1.6375-1.6960.16631390.12692636X-RAY DIFFRACTION100
1.696-1.76390.16621380.12722612X-RAY DIFFRACTION100
1.7639-1.84420.14821380.12752637X-RAY DIFFRACTION100
1.8442-1.94140.17831390.13082635X-RAY DIFFRACTION100
1.9414-2.0630.17031390.13582641X-RAY DIFFRACTION100
2.063-2.22230.16781400.13392656X-RAY DIFFRACTION99
2.2223-2.44590.16871380.14382620X-RAY DIFFRACTION99
2.4459-2.79970.18851380.1552630X-RAY DIFFRACTION99
2.7997-3.52680.17251420.1572691X-RAY DIFFRACTION99
3.5268-35.51870.1581440.15182732X-RAY DIFFRACTION99

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