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- PDB-4zfx: Siderocalin-mediated recognition and cellular uptake of actinides -

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Basic information

Entry
Database: PDB / ID: 4zfx
TitleSiderocalin-mediated recognition and cellular uptake of actinides
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsMetal Binding Protein/inhibitor / Metal Binding Protein-inhibitor complex
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 beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-EB4 / THORIUM ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsAllred, B.E. / Rupert, P.B. / Gauny, S.S. / An, D.D. / Ralston, C.Y. / Sturzbecher-Hoehne, M. / Strong, R.K. / Abergel, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides.
Authors: Allred, B.E. / Rupert, P.B. / Gauny, S.S. / An, D.D. / Ralston, C.Y. / Sturzbecher-Hoehne, M. / Strong, R.K. / Abergel, R.J.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.4Nov 13, 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
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2339
Polymers62,1023
Non-polymers2,1316
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-5 kcal/mol
Surface area26690 Å2
Unit cell
Length a, b, c (Å)114.530, 114.530, 119.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA8 - 17610 - 178
21ILEILEBB8 - 17610 - 178
12SERSERAA5 - 1767 - 178
22SERSERCC5 - 1767 - 178
13ILEILEBB8 - 17610 - 178
23ILEILECC8 - 17610 - 178

NCS ensembles :
ID
1
2
3

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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: 20700.564 Da / Num. of mol.: 3 / Fragment: residues 24-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P80188
#2: Chemical ChemComp-TH / THORIUM ION


Mass: 232.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Th
#3: Chemical ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin


Mass: 669.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O15
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4 / Details: NaCl, Li2SO4, Acetate, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 26474 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.082 / Χ2: 1.883 / Net I/av σ(I): 27.788 / Net I/σ(I): 17.5 / Num. measured all: 200751
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.596.70.4912891.489100
2.59-2.647.90.46212951.50299.9
2.64-2.697.90.39112991.542100
2.69-2.757.90.32812991.624100
2.75-2.817.90.27513171.618100
2.81-2.8780.26212991.6999.9
2.87-2.947.90.19713091.803100
2.94-3.027.90.17112941.918100
3.02-3.1180.13913142.10899.9
3.11-3.2180.1313052.073100
3.21-3.337.80.11113152.281100
3.33-3.467.70.09813242.38799.9
3.46-3.627.70.0913092.24599.9
3.62-3.817.50.08313372.467100
3.81-4.057.50.06813212.1399.5
4.05-4.367.40.06113351.81799.8
4.36-4.87.30.05613431.74599.4
4.8-5.497.20.0613551.8599.8
5.49-6.926.90.06113801.65999.8
6.92-506.60.04614351.59996.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM6

1lm6


Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2619 / WRfactor Rwork: 0.2277 / FOM work R set: 0.8 / SU B: 16.495 / SU ML: 0.2 / SU R Cruickshank DPI: 0.4516 / SU Rfree: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1330 5.1 %RANDOM
Rwork0.2397 ---
obs0.2412 24968 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.41 Å2 / Biso mean: 57.594 Å2 / Biso min: 19.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 39 21 4213
Biso mean--50.62 34.25 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024316
X-RAY DIFFRACTIONr_bond_other_d0.0050.024030
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9665865
X-RAY DIFFRACTIONr_angle_other_deg1.17739268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41424.378201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88915713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0431519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214886
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021035
X-RAY DIFFRACTIONr_mcbond_it1.5852.9112067
X-RAY DIFFRACTIONr_mcbond_other1.5852.912066
X-RAY DIFFRACTIONr_mcangle_it2.4934.3622579
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91410.11
12B91410.11
21A98750.11
22C98750.11
31B91860.12
32C91860.12
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 95 -
Rwork0.306 1819 -
all-1914 -
obs--99.53 %
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)
12.7398-1.56080.07883.83320.02562.51520.18320.14290.0520.0053-0.14920.0065-0.1939-0.2833-0.0340.07190.06180.03410.0979-0.01570.080130.349774.897158.1627
22.8846-2.3620.45595.93090.30963.3216-0.02390.57720.06520.5611-0.18870.27720.0935-0.44940.21260.508-0.2039-0.06460.7240.03370.328253.415197.620833.6713
33.5475-0.19440.29432.61830.15073.02910.01130.2323-0.2053-0.1462-0.0175-0.06620.2045-0.06920.00620.0233-0.00530.00570.0178-0.01410.014447.126646.621742.1879
40000000000000000.2754000.275400.2754000
50000000000000000.2754000.275400.2754000
60000000000000000.2754000.275400.2754000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 177
2X-RAY DIFFRACTION2B8 - 177
3X-RAY DIFFRACTION3C5 - 177
4X-RAY DIFFRACTION4D1
5X-RAY DIFFRACTION5D2
6X-RAY DIFFRACTION6D3

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