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- PDB-8uz9: Fundamental Characterization of Chelated and Crystallized Actiniu... -

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Basic information

Entry
Database: PDB / ID: 8uz9
TitleFundamental Characterization of Chelated and Crystallized Actinium in a Macromolecular Host
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsMETAL BINDING PROTEIN / inhibitor
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / enterobactin binding / iron ion sequestering activity / 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 ...siderophore transport / Metal sequestration by antimicrobial proteins / enterobactin binding / iron ion sequestering activity / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Chem-4OL / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å
AuthorsRupert, P.B. / Strong, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Actinium chelation and crystallization in a macromolecular scaffold.
Authors: Wacker, J.N. / Woods, J.J. / Rupert, P.B. / Peterson, A. / Allaire, M. / Lukens, W.W. / Gaiser, A.N. / Minasian, S.G. / Strong, R.K. / Abergel, R.J.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)64,83012
Polymers61,6693
Non-polymers3,1619
Water55831
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5343
Polymers20,5561
Non-polymers9782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5343
Polymers20,5561
Non-polymers9782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7626
Polymers20,5561
Non-polymers1,2055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.855, 114.855, 119.273
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-ID
11
22
33
/ 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


Mass: 20556.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P80188

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Non-polymers , 5 types, 40 molecules

#2: Chemical ChemComp-ZTM / Actinium Ion


Mass: 227.000 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ac / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4OL / N,N'-butane-1,4-diylbis[1-hydroxy-N-(3-{[(1-hydroxy-6-oxo-1,6-dihydropyridin-2-yl)carbonyl]amino}propyl)-6-oxo-1,6-dihydropyridine-2-carboxamide]


Mass: 750.712 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H38N8O12
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Acetate (pH 4), Li2SO4, NaCl, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→82.77 Å / Num. obs: 48793 / % possible obs: 96.2 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 0.84 / Net I/σ(I): 8.5 / Num. measured all: 301926
Reflection shellResolution: 2.04→2.1 Å / % possible obs: 97.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.509 / Num. measured all: 22673 / Num. unique obs: 3829 / CC1/2: 0.854 / Rpim(I) all: 0.22 / Rrim(I) all: 0.558 / Χ2: 0.55 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
pointlessdata scaling
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.08→48.12 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.425 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25478 2438 5.1 %RANDOM
Rwork0.22457 ---
obs0.22603 45773 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.08→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 93 31 4239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134325
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174002
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6765877
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5959202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46223.27211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76815696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0591517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021039
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_it3.6814.6292065
X-RAY DIFFRACTIONr_mcbond_other3.6754.6292064
X-RAY DIFFRACTIONr_mcangle_it5.2216.9122576
X-RAY DIFFRACTIONr_mcangle_other5.2216.9132577
X-RAY DIFFRACTIONr_scbond_it4.615.1722260
X-RAY DIFFRACTIONr_scbond_other4.5425.1552253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.897.5553290
X-RAY DIFFRACTIONr_long_range_B_refined9.15252.5364502
X-RAY DIFFRACTIONr_long_range_B_other9.1552.5184501
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)
11A50660.1
12B50660.1
21A52720.11
22C52720.11
31B50800.09
32C50800.09
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 160 -
Rwork0.261 3094 -
obs--92.18 %
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)
10.7673-0.7389-0.17591.40650.25210.38990.14660.1253-0.0218-0.0071-0.1297-0.0284-0.0635-0.0933-0.01690.15880.05910.02790.1735-0.00950.226630.175374.777357.7587
22.3184-2.6928-1.13565.70921.31461.80270.12770.724-0.09370.5171-0.51750.00080.2503-0.39990.38970.3605-0.0701-0.00380.50390.01980.115853.811497.666633.8809
30.7482-0.06880.1810.348-0.20560.8028-0.03880.0566-0.0232-0.0199-0.0153-0.01980.0574-0.03180.05410.1613-0.01660.02220.175-0.01380.230747.260746.543742.1449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 201
2X-RAY DIFFRACTION2B5 - 201
3X-RAY DIFFRACTION3C5 - 201

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