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

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Basic information

Entry
Database: PDB / ID: 8uyn
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 / LANTHANUM (III) ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)64,73711
Polymers61,6693
Non-polymers3,0678
Water3,009167
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4463
Polymers20,5561
Non-polymers8902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5424
Polymers20,5561
Non-polymers9863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7484
Polymers20,5561
Non-polymers1,1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.148, 116.148, 117.562
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, 175 molecules

#2: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: La
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Acetate (pH 4), NaCl, Li2SO4, 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: 1.031 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.031 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55159 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.025 / Rrim(I) all: 0.084 / Χ2: 1.441 / Net I/σ(I): 8.6 / Num. measured all: 634718
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.0311.90.48327100.9470.9860.1460.5050.675100
2.03-2.0711.70.52327090.9280.9810.160.5470.945100
2.07-2.1111.60.4627030.9360.9830.1420.4811.253100
2.11-2.1511.70.35127320.9670.9920.1070.3680.918100
2.15-2.211.60.3127020.9720.9930.0950.3240.888100
2.2-2.2510.80.41527090.9590.9890.1350.4371.559100
2.25-2.319.60.35327370.9640.9910.1220.3751.76499.5
2.31-2.3711.30.21327150.9850.9960.0660.2230.992100
2.37-2.4412.30.18927290.9880.9970.0560.1971.078100
2.44-2.5212.20.16927260.990.9970.050.1761.169100
2.52-2.6112.10.1527430.9910.9980.0450.1571.237100
2.61-2.7111.90.14227530.9920.9980.0430.1481.464100
2.71-2.8411.70.11627400.9950.9990.0350.1211.487100
2.84-2.9910.70.09827450.9960.9990.0310.1031.596100
2.99-3.17120.08427780.9970.9990.0250.0881.82100
3.17-3.4212.30.07327630.9980.9990.0220.0762.001100
3.42-3.7611.50.06928010.9970.9990.0210.0722.583100
3.76-4.3110.50.05627960.99810.0180.0592.331100
4.31-5.4311.80.04428460.99910.0130.0461.69199.9
5.43-50110.03730220.99910.0120.0391.47399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→47.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.296 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22718 2714 4.9 %RANDOM
Rwork0.20376 ---
obs0.20496 52322 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å2-0 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 2→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 188 167 4487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174172
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.7046144
X-RAY DIFFRACTIONr_angle_other_deg1.2481.6159614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24823.288219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1271518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
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_it1.3752.4492083
X-RAY DIFFRACTIONr_mcbond_other1.3642.4482082
X-RAY DIFFRACTIONr_mcangle_it2.2323.6542603
X-RAY DIFFRACTIONr_mcangle_other2.2323.6552604
X-RAY DIFFRACTIONr_scbond_it1.622.7672426
X-RAY DIFFRACTIONr_scbond_other1.622.7622423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.664.0693527
X-RAY DIFFRACTIONr_long_range_B_refined4.54628.6494824
X-RAY DIFFRACTIONr_long_range_B_other4.49228.4994802
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)
11A53040.08
12B53040.08
21A53290.09
22C53290.09
31B52270.09
32C52270.09
LS refinement shellResolution: 2→2.048 Å
RfactorNum. reflection% reflection
Rfree0.274 184 -
Rwork0.211 3763 -
obs--98.72 %
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)
11.3183-0.75940.21793.10970.69172.11950.0529-0.0075-0.06850.0731-0.1361-0.0197-0.0789-0.37120.08320.02590.03120.00540.0975-0.0040.047230.429775.42157.1945
21.77350.06080.0841.5126-0.71663.13660.09620.11-0.0925-0.0754-0.0395-0.010.12880.1182-0.05670.04930.0455-0.02980.0429-0.0290.020752.2475100.1535.4187
31.67990.10210.35761.2841-0.32131.8346-0.00180.0881-0.0509-0.0058-0.0145-0.04610.1510.00270.01630.0164-0.007-0.00010.01750.00920.025747.233946.976341.4308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 301
2X-RAY DIFFRACTION2B6 - 301
3X-RAY DIFFRACTION3C5 - 301

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