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- PDB-4iax: Engineered human lipocalin 2 (CL31) in complex with Y-DTPA -

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Basic information

Entry
Database: PDB / ID: 4iax
TitleEngineered human lipocalin 2 (CL31) in complex with Y-DTPA
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / beta-barrel / engineered lipocalin / binding protein / Y-CHX-A''-DTPA / Strep-tag
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: 1.9 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structure-guided engineering of Anticalins with improved binding behavior and biochemical characteristics for application in radio-immuno imaging and/or therapy
Authors: Eggenstein, E. / Eichinger, A. / Kim, H.J. / Skerra, A.
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3703
Polymers21,5651
Non-polymers8052
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.120, 60.120, 110.550
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 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: 21565.494 Da / Num. of mol.: 1 / Fragment: UNP residues 21-198
Mutation: Q28H,V33Q,L36R,I41A,L42P,R43P,E44M,K46P,D47E,P48L,Q49L,K50L,M51L,Y52T,T54Q,I55T,N65D,S68A,L70R,K75M,D77E,W79L,I80T,R81M,G86S,C87P,S99N,L107F,S127Q,K134S,T136S,Y138L,T145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL / Plasmid: pNGAL15-CL31 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F- / References: UniProt: P80188
#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.: 1 / Source method: obtained synthetically / Formula: C30H45N5O13S
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.32 Å3/Da / Density % sol: 46.89 % / Mosaicity: 1.19 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.65
Details: 17%(w/v) PEG3350, 0.4M potassium phosphate, pH 4.65, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2009 / Details: mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→52.82 Å / Num. all: 16702 / Num. obs: 16692 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rsym value: 0.068 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-27.50.2630.2452.81800423880.0960.2630.2457.5100
2-2.127.60.1880.1753.81712522520.0680.1880.17510.5100
2.12-2.277.60.1490.1394.81601321090.0540.1490.13912.5100
2.27-2.457.60.1070.16.91530520060.0390.1070.114.8100
2.45-2.697.60.0880.0828.11399818380.0320.0880.08217.3100
2.69-37.60.060.05611.81280316920.0210.060.05622.3100
3-3.477.50.050.04713.21120014900.0180.050.04728.3100
3.47-4.257.40.0590.05510.4952812930.0220.0590.05533.8100
4.25-6.017.20.0520.04911.3740510290.0190.0520.04934.7100
6.01-19.8396.20.0380.03416.636765950.0150.0380.03429.896.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.84 Å
Translation2.5 Å19.84 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSZ

3dsz


Resolution: 1.9→52.82 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2446 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8324 / SU B: 3.303 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1517 / SU Rfree: 0.1484 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 843 5.1 %RANDOM
Rwork0.1947 ---
obs0.1972 16635 99.79 %-
all-16702 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.11 Å2 / Biso mean: 22.3231 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 43 116 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221477
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9412004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44524.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.024157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211137
X-RAY DIFFRACTIONr_mcbond_it1.2161.5865
X-RAY DIFFRACTIONr_mcangle_it2.11221411
X-RAY DIFFRACTIONr_scbond_it3.5673612
X-RAY DIFFRACTIONr_scangle_it5.664.5593
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 70 -
Rwork0.219 1138 -
all-1208 -
obs--100 %

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