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- PDB-4iaw: Engineered human lipocalin 2 (C26) in complex with Y-DTPA -

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Basic information

Entry
Database: PDB / ID: 4iaw
TitleEngineered human lipocalin 2 (C26) 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


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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: 2.4 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1359
Polymers64,7213
Non-polymers2,4146
Water2,720151
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3783
Polymers21,5741
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3783
Polymers21,5741
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3783
Polymers21,5741
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.260, 113.260, 119.980
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: 21573.502 Da / Num. of mol.: 3 / Fragment: UNP residues 21-198
Mutation: Q28H,V33Q,L36R,I41A,L42P,P48L,Q49L,Y52T,T54Q,I55T,S68A,L70R,K75M,D77E,W79L,I80T,R81M,C87S,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-C26 / 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.: 3 / Source method: obtained synthetically / Formula: C30H45N5O13S
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.97 Å3/Da / Density % sol: 58.62 % / Mosaicity: 0.52 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2M dipotassium phosphate, 0.2M lithium sulfate, 0.1M CAPS/NaOH, pH 10.5, VAPOR DIFFUSION, SITTING 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: 2.4→82.36 Å / Num. all: 31147 / Num. obs: 31127 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Rsym value: 0.085 / Net I/σ(I): 24.7
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
2.4-2.5314.80.3810.3682.16629844700.0990.3810.3688.5100
2.53-2.6814.80.2970.2862.76251442200.0770.2970.28610.5100
2.68-2.8714.80.1940.1874.15906639910.050.1940.18715.1100
2.87-3.114.80.1230.1196.45515237300.0320.1230.11921.1100
3.1-3.3914.70.0770.07410.15088334500.020.0770.07427.7100
3.39-3.7914.60.0590.05711.74603831430.0150.0590.05735100
3.79-4.3814.60.0750.07284060727870.0190.0750.07240.4100
4.38-5.3714.40.0810.0797.33445323920.0210.0810.07943.3100
5.37-7.59140.0420.04113.62655218930.0110.0420.04143.5100
7.59-19.99712.10.0290.02815.61271810510.0080.0290.02841.694.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.04 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.94 Å
Translation2.5 Å19.94 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: 3DTQ

3dtq


Resolution: 2.4→82.36 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.2694 / WRfactor Rwork: 0.2224 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8256 / SU B: 6.326 / SU ML: 0.157 / SU R Cruickshank DPI: 0.3448 / SU Rfree: 0.2562 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.346 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 1567 5 %RANDOM
Rwork0.2238 ---
obs0.2262 31073 99.76 %-
all-31127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.73 Å2 / Biso mean: 44.0647 Å2 / Biso min: 3.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→82.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 129 151 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224490
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9936070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42724.402209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24315772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5351524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213425
X-RAY DIFFRACTIONr_mcbond_it0.8141.52641
X-RAY DIFFRACTIONr_mcangle_it1.55924288
X-RAY DIFFRACTIONr_scbond_it2.32231849
X-RAY DIFFRACTIONr_scangle_it3.8894.51782
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 128 -
Rwork0.232 2147 -
all-2275 -
obs--100 %

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