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

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Basic information

Entry
Database: PDB / ID: 4zhc
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 / iron ion sequestering activity / enterobactin 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 ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin 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
ACETATE ION / Chem-TC2 / THORIUM ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 24, 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

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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)64,77513
Polymers62,1023
Non-polymers2,67310
Water2,162120
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5474
Polymers20,7011
Non-polymers8473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4883
Polymers20,7011
Non-polymers7882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7396
Polymers20,7011
Non-polymers1,0395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.657, 114.657, 119.226
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASPAA6 - 1778 - 179
21ASPASPASPASPBB6 - 1778 - 179
12THRTHRILEILEAA4 - 1766 - 178
22THRTHRILEILECC4 - 1766 - 178
13ASPASPASPASPBB6 - 1778 - 179
23ASPASPASPASPCC6 - 1778 - 179

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: residues 24-198
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

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Non-polymers , 5 types, 130 molecules

#2: Chemical ChemComp-TH / THORIUM ION


Mass: 232.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Th
#3: Chemical ChemComp-TC2 / N-{2-[bis(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)amino]ethyl}-1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide / Tren bis-2,3-catecholamido mono-N-hydroxypyridin-2-one-6-amide


Mass: 555.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29N5O9
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4 / Details: NaCl, Li2SO4, Acetate, Ammonium Sulfate / PH range: 4

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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: Feb 6, 2014
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 51169 / % possible obs: 99.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.097 / Χ2: 1.65 / Net I/av σ(I): 25.364 / Net I/σ(I): 19.2 / Num. measured all: 488919
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.04-2.088.70.48824301.42997
2.08-2.119.70.39825231.426100
2.11-2.159.70.37125221.437100
2.15-2.29.70.31725301.49100
2.2-2.259.70.29325371.554100
2.25-2.39.70.24725321.604100
2.3-2.359.80.22825251.629100
2.35-2.429.80.20225331.662100
2.42-2.499.70.17925381.663100
2.49-2.579.80.16325461.696100
2.57-2.669.70.14825381.721100
2.66-2.779.70.12925421.719100
2.77-2.899.70.11525661.713100
2.89-3.059.70.10125591.689100
3.05-3.249.70.09625751.738100
3.24-3.499.60.09525741.793100
3.49-3.849.50.10325992.117100
3.84-4.399.40.10526062.36599.7
4.39-5.5490.07826471.48499.8
5.54-508.70.04927471.01797.6

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Processing

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

1lm6


Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2433 / WRfactor Rwork: 0.2186 / FOM work R set: 0.8627 / SU B: 6.371 / SU ML: 0.089 / SU R Cruickshank DPI: 0.161 / SU Rfree: 0.1431 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2591 5.1 %RANDOM
Rwork0.2063 ---
obs0.2074 48494 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.47 Å2 / Biso mean: 49.072 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 89 120 4355
Biso mean--64.32 44.26 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024367
X-RAY DIFFRACTIONr_bond_other_d0.0010.024071
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.9765933
X-RAY DIFFRACTIONr_angle_other_deg0.64539354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5424.35200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26815710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6681519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214951
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021057
X-RAY DIFFRACTIONr_mcbond_it2.2242.4472074
X-RAY DIFFRACTIONr_mcbond_other2.2022.4432071
X-RAY DIFFRACTIONr_mcangle_it2.9943.6432585
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91160.13
12B91160.13
21A100700.11
22C100700.11
31B93310.12
32C93310.12
LS refinement shellResolution: 2.04→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 207 -
Rwork0.221 3465 -
all-3672 -
obs--98.16 %
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)
12.6428-1.3491-0.00783.51940.44182.08260.14860.11280.01730.0209-0.10840.0075-0.1392-0.1779-0.04030.07320.07470.0280.1055-0.00310.069430.288274.910257.8554
23.2785-1.0629-0.17064.47520.82062.96220.08310.31990.22610.0505-0.13980.2233-0.0785-0.33570.05670.3138-0.0694-0.0020.47960.00350.244553.908597.350833.5925
33.0019-0.26090.32332.0712-0.20792.4735-0.04670.1593-0.2052-0.1467-0.019-0.03920.235-0.04040.06570.0347-0.01270.01640.0263-0.01690.019547.158146.617442.0581
400000000.00010.000200-0.0001-0.00030.00010.00010.5176-0.0498-0.14470.37020.20390.476728.272177.36166.4566
500000000.00010.00050-0.0001-0.0002-0.00060.00030.00010.86740.01660.02020.95390.32740.756456.0701106.708136.6091
60000000-0.00010.000300.0001-0.000300.0001-0.00010.1863-0.1058-0.07550.3713-0.36360.815248.481938.236542.3598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 178
2X-RAY DIFFRACTION2B6 - 177
3X-RAY DIFFRACTION3C4 - 177
4X-RAY DIFFRACTION4A200
5X-RAY DIFFRACTION5B200
6X-RAY DIFFRACTION6C200

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