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- PDB-5khp: Tightening the Recognition of Tetravalent Zr and Th Complexes by ... -

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Basic information

Entry
Database: PDB / ID: 5khp
TitleTightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding Mammalian Protein Siderocalin for Theranostic Applications
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsMETAL BINDING PROTEIN / Siderophore-Binding / NGAL
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-7K9 / ZIRCONIUM ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRupert, P.B. / Strong, R.K.
CitationJournal: Inorg Chem / Year: 2016
Title: Engineered Recognition of Tetravalent Zirconium and Thorium by Chelator-Protein Systems: Toward Flexible Radiotherapy and Imaging Platforms.
Authors: Captain, I. / Deblonde, G.J. / Rupert, P.B. / An, D.D. / Illy, M.C. / Rostan, E. / Ralston, C.Y. / Strong, R.K. / Abergel, R.J.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)65,47618
Polymers62,1023
Non-polymers3,37515
Water95553
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9237
Polymers20,7011
Non-polymers1,2226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5393
Polymers20,7011
Non-polymers8382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0158
Polymers20,7011
Non-polymers1,3147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.383, 114.383, 117.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPCYSCYSAA6 - 1758 - 177
21ASPASPCYSCYSBB6 - 1758 - 177
12SERSERASPASPAA5 - 1777 - 179
22SERSERASPASPCC5 - 1777 - 179
13ASPASPCYSCYSBB6 - 1758 - 177
23ASPASPCYSCYSCC6 - 1758 - 177

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#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: 20700.564 Da / Num. of mol.: 3 / Fragment: UNP residues 21-198
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

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Non-polymers , 5 types, 68 molecules

#2: Chemical ChemComp-ZR / ZIRCONIUM ION / Zirconium


Mass: 91.224 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zr
#3: Chemical ChemComp-7K9 / N,N'-(butane-1,4-diyl)bis(N-{3-[(2,3-dihydroxybenzene-1-carbonyl)amino]propyl}-2,3-dihydroxybenzamide)


Mass: 746.760 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H42N4O12
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Acetate, Li2SO4, NaCl, ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 22217 / % possible obs: 95.4 % / Redundancy: 8.1 % / Net I/σ(I): 28.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM6

1lm6


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.916 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.28 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22784 1219 5.5 %RANDOM
Rwork0.20774 ---
obs0.20884 20976 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 85 53 4201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024256
X-RAY DIFFRACTIONr_bond_other_d0.0040.023876
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9715799
X-RAY DIFFRACTIONr_angle_other_deg0.89138875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.125516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47924.096188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.081518
X-RAY DIFFRACTIONr_chiral_restr0.0470.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214831
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021024
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4543.6692067
X-RAY DIFFRACTIONr_mcbond_other3.4543.6692066
X-RAY DIFFRACTIONr_mcangle_it5.7075.492579
X-RAY DIFFRACTIONr_mcangle_other5.7065.4912580
X-RAY DIFFRACTIONr_scbond_it4.21842188
X-RAY DIFFRACTIONr_scbond_other4.21442188
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7035.8853220
X-RAY DIFFRACTIONr_long_range_B_refined9.62329.1184443
X-RAY DIFFRACTIONr_long_range_B_other9.62329.1234444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A176380.09
12B176380.09
21A195440.08
22C195440.08
31B177420.09
32C177420.09
LS refinement shellResolution: 2.646→2.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 76 -
Rwork0.287 1528 -
obs--95.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2079-0.4038-0.16951.16440.08360.79810.03090.0861-0.0021-0.0015-0.0542-0.0633-0.0228-0.02570.02330.11980.02590.04580.1058-0.00420.162829.635474.309155.8292
22.1-1.4883-1.88752.15681.39563.371-0.29350.58730.34030.46370.2425-0.34950.6902-0.58420.0510.2541-0.0592-0.04210.55290.04650.136652.947197.299734.5459
30.7167-0.24680.12810.4252-0.08820.4403-0.03380.0613-0.01530.0524-0.0072-0.00980.0438-0.04720.04090.1062-0.01140.02350.1274-0.01340.167246.886646.132441.1703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 177
2X-RAY DIFFRACTION2B6 - 176
3X-RAY DIFFRACTION3C5 - 177

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