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

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Basic information

Entry
Database: PDB / ID: 4zhd
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-4OZ / PLUTONIUM ION / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / diffrn_radiation_wavelength / 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 1.4Oct 16, 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)64,06013
Polymers62,1023
Non-polymers1,95810
Water1,72996
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3204
Polymers20,7011
Non-polymers6193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2283
Polymers20,7011
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5126
Polymers20,7011
Non-polymers8115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.589, 114.589, 118.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-337-

HOH

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
11ASPASPAA6 - 1768 - 178
21ASPASPBB6 - 1768 - 178
12THRTHRAA4 - 1766 - 178
22THRTHRCC4 - 1766 - 178
13ASPASPBB6 - 1768 - 178
23ASPASPCC6 - 1768 - 178

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 23-197 / Mutation: C87S
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, 106 molecules

#2: Chemical ChemComp-4PU / PLUTONIUM ION


Mass: 244.000 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pu
#3: Chemical ChemComp-4OZ / methyl N-(2,3-dihydroxybenzoyl)-O-formyl-L-serinate


Type: peptide-like / Mass: 283.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13NO7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.21 Å3/Da / Density % sol: 61.66 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 49864 / % possible obs: 99.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.804 / Net I/av σ(I): 38.243 / Net I/σ(I): 22.1 / Num. measured all: 472916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.097.30.36823411.62395.3
2.09-2.129.10.30424791.568100
2.12-2.169.70.27924621.58100
2.16-2.219.80.24624851.63499.9
2.21-2.269.70.22824711.78999.9
2.26-2.319.80.20324571.84899.9
2.31-2.379.70.17924841.82399.9
2.37-2.439.70.15624971.89199.8
2.43-2.59.70.13724901.93799.8
2.5-2.589.70.12424832.00599.8
2.58-2.689.70.10924732.03399.6
2.68-2.789.70.08924952.06299.5
2.78-2.919.70.08225062.17299.4
2.91-3.069.70.06824791.87499.4
3.06-3.259.70.06125071.80299.2
3.25-3.519.60.05425091.75899.1
3.51-3.869.60.05525231.53498.9
3.86-4.429.50.05825271.65498.5
4.42-5.569.20.04725491.64198.1
5.56-508.90.03726471.76595.8

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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: 2.05→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2299 / WRfactor Rwork: 0.2149 / FOM work R set: 0.8567 / SU B: 6.901 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1621 / SU Rfree: 0.1429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / 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
Rfree0.2257 2526 5.1 %RANDOM
Rwork0.2036 ---
obs0.2047 47305 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116 Å2 / Biso mean: 44.457 Å2 / Biso min: 18.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 85 96 4325
Biso mean--59.2 37.9 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024358
X-RAY DIFFRACTIONr_bond_other_d0.0020.024062
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9755925
X-RAY DIFFRACTIONr_angle_other_deg0.75439328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59924.188191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8415702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6871518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214918
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021043
X-RAY DIFFRACTIONr_mcbond_it2.7172.2012089
X-RAY DIFFRACTIONr_mcbond_other2.7112.22088
X-RAY DIFFRACTIONr_mcangle_it3.5233.2752608
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A9397
12B9397
21A9498
22C9498
31B9636
32C9636
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 188 -
Rwork0.223 3357 -
all-3545 -
obs--97.71 %
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)
12.6265-1.25360.35383.1680.31131.99260.17290.10.05570.0333-0.1149-0.0669-0.0608-0.1752-0.05810.0670.06310.01840.0866-0.0030.085630.223774.819457.5249
22.8729-0.75690.35393.80570.91083.05450.10870.11470.05590.0771-0.12220.2317-0.1693-0.34410.01340.2953-0.0501-0.00160.3931-0.00340.215753.701897.500633.7849
32.8171-0.43690.22542.0247-0.37012.555-0.020.1268-0.1871-0.1292-0.0171-0.00840.265-0.03340.03710.0339-0.00750.01180.0125-0.01870.028747.179946.648342.0043
4000000000.00010000000.24920.0408-0.00150.30630.05430.27627.864576.944465.6131
5000000000.000300-0.0002-0.00050.000200.7305-0.03950.09320.68350.08990.563356.369105.773935.7936
60000000-0.00010.000400.0001-0.0004-0.00010.0001-0.00010.1708-0.21820.06130.449-0.50421.087448.264938.553742.0537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 177
2X-RAY DIFFRACTION2B6 - 177
3X-RAY DIFFRACTION3C4 - 177
4X-RAY DIFFRACTION4A200
5X-RAY DIFFRACTION5B200
6X-RAY DIFFRACTION6C200

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