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- PDB-3dsz: Engineered human lipocalin 2 in complex with Y-DTPA -

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Basic information

Entry
Database: PDB / ID: 3dsz
TitleEngineered human lipocalin 2 in complex with Y-DTPA
Componentsengineered human lipocalin 2
KeywordsTRANSPORT PROTEIN / protein design / ligand binding protein / beta barrel / engineered lipocalin / de novo protein / protein binding
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 / response to blue light ...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 / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / 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-LIZ / YTTRIUM (III) ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2
Authors: Kim, H.J. / Eichinger, A. / Skerra, A.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: engineered human lipocalin 2
B: engineered human lipocalin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2986
Polymers42,6882
Non-polymers1,6094
Water5,909328
1
A: engineered human lipocalin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1493
Polymers21,3441
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: engineered human lipocalin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1493
Polymers21,3441
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 82.350, 115.128
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 engineered human lipocalin 2 / neutrophil gelatinase-associated lipocalin / NGAL / siderocalin


Mass: 21344.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, variant Tb7.N9 / Plasmid: pNGAL15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P80188*PLUS
#2: Chemical ChemComp-LIZ / N-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)amino]-3-[4-({[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]carbamothioyl}amino)phenyl]propyl}glycine


Mass: 715.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H45N5O13S
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22% polyethylene glycol 3350, 0.1M Bistris/HCl, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→66.979 Å / Num. obs: 26827 / % possible obs: 98.2 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 6.1 / Num. unique all: 3813 / Rsym value: 0.372 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.423 / Cor.coef. Fo:Fc: 0.579
Highest resolutionLowest resolution
Rotation3 Å38.78 Å
Translation3 Å38.78 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.864 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1347 4.9 %RANDOM
Rwork0.213 ---
all-27437 --
obs-26807 97.7 %-
Solvent computationBsol: 56.905 Å2
Displacement parametersBiso max: 81.5 Å2 / Biso mean: 27.759 Å2 / Biso min: 11.34 Å2
Baniso -1Baniso -2Baniso -3
1-2.184 Å20 Å20 Å2
2--2.184 Å20 Å2
3----4.367 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 100 328 3216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4021.5
X-RAY DIFFRACTIONc_scbond_it2.1722
X-RAY DIFFRACTIONc_mcangle_it2.1872
X-RAY DIFFRACTIONc_scangle_it3.3312.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3DTPA-Tris-noY.param
X-RAY DIFFRACTION4ion.param

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