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- PDB-1kxo: ENGINEERED LIPOCALIN DIGA16 : APO-FORM -

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Basic information

Entry
Database: PDB / ID: 1kxo
TitleENGINEERED LIPOCALIN DIGA16 : APO-FORM
ComponentsDigA16
KeywordsLIGAND BINDING PROTEIN / pieris brassicae / lipocalin / anticalin / genetical engineering / digoxigenin
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / extracellular region / cytoplasm
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Bilin-binding protein
Similarity search - Component
Biological speciesPieris brassicae (large cabbage white)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsKorndoerfer, I.P. / Skerra, A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin.
Authors: Korndoerfer, I.P. / Schlehuber, S. / Skerra, A.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: A Novel Type of Receptor Protein, based on the Lipocalin Scaffold, with Specificity for Digoxigenin
Authors: Schlehuber, S. / Beste, G. / Skerra, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Small Antibody-like Proteins with Prescribed Ligand Specificities Derived from the Lipocalin Fold.
Authors: Beste, G. / Schmidt, F.S. / Stibora, T. / Skerra, A.
History
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DigA16


Theoretical massNumber of molelcules
Total (without water)20,8331
Polymers20,8331
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.873, 63.476, 38.191
Angle α, β, γ (deg.)90.00, 92.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DigA16 / BILIN BINDING PROTEIN / BBP / DIGA16 ANTICALIN


Mass: 20833.158 Da / Num. of mol.: 1
Mutation: N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M
Source method: isolated from a genetically manipulated source
Details: genetically engineered variant of bilin binding protein
Source: (gene. exp.) Pieris brassicae (large cabbage white) / Plasmid: pbbp21-diga16 / Production host: Escherichia coli (E. coli) / Strain (production host): jm83 / References: UniProt: P09464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1-M Hepes, 10% Isopropanole, 19% PEG 4000, pH = 7.8, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mM(w/v)HEPES-NaOH1droppH7.6-8.0
30.1 MHEPES-NaOH1reservoir
410 %isopropanol1reservoir
524 %PEG40001reservoirpH7.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2001
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→48.22 Å / Num. all: 14754 / Num. obs: 14754 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rsym value: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1260 / Rsym value: 0.2 / % possible all: 77.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 99 Å / Num. measured all: 72064 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 77.2 % / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: The structure of diga16 in presence of digoxigenin

Resolution: 1.8→48.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.518 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.176 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 726 4.9 %RANDOM
Rwork0.209 ---
obs0.21229 14674 89.45 %-
all-14674 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.1 Å2
2---2.68 Å20 Å2
3---2.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 104 1424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211352
X-RAY DIFFRACTIONr_bond_other_d0.0010.021128
X-RAY DIFFRACTIONr_angle_refined_deg2.6841.9221834
X-RAY DIFFRACTIONr_angle_other_deg1.31632643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8653161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96815214
X-RAY DIFFRACTIONr_chiral_restr0.1620.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021496
X-RAY DIFFRACTIONr_gen_planes_other0.010.02285
X-RAY DIFFRACTIONr_nbd_refined0.2490.3278
X-RAY DIFFRACTIONr_nbd_other0.2050.31090
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.322
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it5.6722812
X-RAY DIFFRACTIONr_mcangle_it7.39431305
X-RAY DIFFRACTIONr_scbond_it6.4092540
X-RAY DIFFRACTIONr_scangle_it8.4673529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 46 -
Rwork0.278 892 -
obs--78.63 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.68

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