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- PDB-5nkn: Crystal structure of an Anticalin-colchicine complex -

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Basic information

Entry
Database: PDB / ID: 5nkn
TitleCrystal structure of an Anticalin-colchicine complex
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / beta-barrel / colchicine / Lcn2 / lipocalin / NGAL / protein engineering
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / cellular response to increased oxygen levels ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / cellular response to increased oxygen levels / response to blue light / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / enterobactin binding / iron ion sequestering activity / response to herbicide / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / acute-phase response / Iron uptake and transport / cellular response to nerve growth factor stimulus / response to virus / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / defense response to bacterium / iron ion binding / response to xenobiotic stimulus / innate immune response / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / 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
Chem-LOC / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSkerra, A. / Eichinger, A. / Barkovskiy, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz-Zentrum Berlin Germany
CitationJournal: Biol. Chem. / Year: 2019
Title: An engineered lipocalin that tightly complexes the plant poison colchicine for use as antidote and in bioanalytical applications.
Authors: Barkovskiy, M. / Ilyukhina, E. / Dauner, M. / Eichinger, A. / Skerra, A.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 17, 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
Revision 1.4Oct 23, 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: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3422
Polymers19,9431
Non-polymers3991
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.680, 46.680, 136.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 19942.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6 / Comment: medication, antiinflammatory*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2 M (NH4)2SO4, 200 mM Li2SO4, 100 mM Tris/HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89429 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2016 / Details: coated Si mirror
RadiationMonochromator: Si - 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 1.811→46.68 Å / Num. all: 8323 / Num. obs: 8323 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.099 / Rsym value: 0.094 / Net I/av σ(I): 6.3 / Net I/σ(I): 17 / Num. measured all: 85451
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.3290.411.90.1360.4330.4199.4
2.32-2.469.40.3352.30.1110.3530.335100
2.46-2.63100.243.20.0780.2530.24100
2.63-2.8410.50.1654.60.0530.1740.165100
2.84-3.1111.10.1067.10.0330.1110.106100
3.11-3.4811.30.0828.40.0250.0860.082100
3.48-4.0211.20.07780.0240.0810.077100
4.02-4.9210.90.078.80.0220.0730.07100
4.92-6.9610.50.04613.50.0150.0480.046100
6.96-46.688.70.02920.30.010.0310.02999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.81 Å46.7 Å
Translation1.81 Å46.7 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTQ

3dtq


Resolution: 2.2→46.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.49 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.257
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 420 5.1 %RANDOM
Rwork0.1974 ---
obs0.201 7858 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 164.6 Å2 / Biso mean: 36.407 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2.2→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 29 36 1459
Biso mean--25.34 28.06 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021464
X-RAY DIFFRACTIONr_bond_other_d0.0020.021378
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9781986
X-RAY DIFFRACTIONr_angle_other_deg0.97433179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50524.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35615247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51155
X-RAY DIFFRACTIONr_chiral_restr0.090.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 21 -
Rwork0.244 554 -
all-575 -
obs--98.8 %
Refinement TLS params.Method: refined / Origin x: -11.843 Å / Origin y: 12.749 Å / Origin z: -13.133 Å
111213212223313233
T0.0585 Å20.0177 Å20.015 Å2-0.0348 Å2-0.0553 Å2--0.2815 Å2
L2.2299 °20.6316 °2-2.1459 °2-1.6113 °20.2487 °2--2.7168 °2
S0.2693 Å °0.0726 Å °-0.134 Å °-0.0468 Å °-0.1483 Å °-0.1237 Å °-0.3571 Å °-0.1238 Å °-0.1211 Å °

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