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- PDB-5efw: Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the ... -

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Basic information

Entry
Database: PDB / ID: 5efw
TitleCrystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1
Components
  • NPH1-1
  • Z-dark, a small protein based on the Z domain affibody
KeywordsSIGNALING PROTEIN / LOV domain / photoreceptor / affibody / optogenetic tool
Function / homology
Function and homology information


blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Immunoglobulin FC, subunit C / PAS-associated, C-terminal / PAC domain profile. / PAS domain / 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-associated, C-terminal / PAC domain profile. / PAS domain / 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 / PAS domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 speciesAvena sativa (oats)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWinkler, A. / Wang, H. / Hartmann, E. / Hahn, K. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1279 Germany
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
DepositionOct 26, 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 31, 2018Group: Author supporting evidence / Database references / Category: pdbx_audit_support / pdbx_related_exp_data_set / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NPH1-1
B: Z-dark, a small protein based on the Z domain affibody
C: Z-dark, a small protein based on the Z domain affibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,79510
Polymers29,7623
Non-polymers1,0337
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-93 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 54.700, 188.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NPH1-1


Mass: 16631.729 Da / Num. of mol.: 1 / Fragment: UNP residues 404-546 / Mutation: C450A
Source method: isolated from a genetically manipulated source
Details: Cys450Ala mutation introduced to render the protein light inactive
Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O49003
#2: Protein Z-dark, a small protein based on the Z domain affibody


Mass: 6565.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selected from an in vitro selection from a protein domain library using mRNA display based on the Z domain
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 2 M ammonium sulfate, 0.1 M sodium citrate pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17450 / Num. obs: 17450 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 30.74 Å2 / Rmerge F obs: 0.111 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.115 / Χ2: 0.94 / Net I/σ(I): 10.3 / Num. measured all: 100397
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.26.30.4110.5283.2613973222122200.577100
2.2-2.30.2990.4064.411357184818460.44499.9
2.3-2.40.2470.2975.629309156915670.32799.9
2.4-2.50.2010.2526.47509133713340.27999.8
2.5-2.60.1640.2197.416574114111380.24199.7
2.6-2.70.1440.1858.6157329549530.20399.9
2.7-40.0720.09313.7131686573856910.10399.2
4-100.0390.06519.3213231253624970.07298.5
100.0320.0720.610262152040.07794.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å47.28 Å
Translation2.5 Å47.28 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Coot2.4.0model building
PHENIX(phenix.refine: 1.8_1069)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v1a, 1lp1

2v1a

1lp1


Resolution: 2.1→47.28 Å / FOM work R set: 0.8387 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 873 5 %Random selection
Rwork0.2018 16572 --
obs0.2045 17445 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.65 Å2 / Biso mean: 32.36 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 2.1→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 61 94 2106
Biso mean--41.74 37.77 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082049
X-RAY DIFFRACTIONf_angle_d1.0642777
X-RAY DIFFRACTIONf_chiral_restr0.075306
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d13.312777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.23170.29011410.231526852826100
2.2317-2.4040.28911430.222927162859100
2.404-2.64590.2941440.232727212865100
2.6459-3.02870.31031440.23592749289399
3.0287-3.81560.24661460.19162760290699
3.8156-47.29170.21351550.17512941309698
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)
12.9375-0.7565-0.07273.0123-0.20533.425-0.1253-0.1065-0.21890.08810.0878-0.01850.12460.02450.0130.109-0.0003-0.01030.18270.01050.16340.368110.4853-17.2964
25.272-5.06213.28855.6885-4.78795.92-0.4294-0.56110.38240.90870.3318-0.741-0.31010.00970.02630.20780.0122-0.03030.3467-0.0580.20899.906113.8979-8.6443
33.7828-1.3458-0.52553.662-0.04121.97370.01130.010.51040.0674-0.1639-0.2423-0.33960.06790.12320.35230.0422-0.03940.1514-0.05170.2277-4.81733.2714-24.6081
45.5117-1.79441.85153.8448-1.67494.06480.0110.37320.1719-0.3416-0.069-0.2172-0.36220.14370.06340.339-0.04120.01070.235-0.01660.1519-3.150630.0238-39.0141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 406:521)A406 - 521
2X-RAY DIFFRACTION2chain 'A' and (resseq 522:546)A522 - 546
3X-RAY DIFFRACTION3chain 'C' and (resseq 12:60)C12 - 60
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:60)B6 - 60

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