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

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Basic information

Entry
Database: PDB / ID: 4zhf
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


Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-4OL / CURIUM ION / Gene 8 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Revision 1.4Oct 23, 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
D: Neutrophil gelatinase-associated lipocalin
E: Neutrophil gelatinase-associated lipocalin
F: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,51932
Polymers124,2036
Non-polymers7,31526
Water4,540252
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7944
Polymers20,7011
Non-polymers1,0943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9826
Polymers20,7011
Non-polymers1,2825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9826
Polymers20,7011
Non-polymers1,2825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9826
Polymers20,7011
Non-polymers1,2825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9826
Polymers20,7011
Non-polymers1,2825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7944
Polymers20,7011
Non-polymers1,0943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.676, 117.775, 121.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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
11SERSERILEILEAA3 - 1765 - 178
21SERSERILEILEBB3 - 1765 - 178
12SERSERILEILEAA3 - 1765 - 178
22SERSERILEILECC3 - 1765 - 178
13ASPASPGLYGLYAA2 - 1784 - 180
23ASPASPGLYGLYDD2 - 1784 - 180
14ASPASPILEILEAA2 - 1764 - 178
24ASPASPILEILEEE2 - 1764 - 178
15SERSERILEILEAA3 - 1765 - 178
25SERSERILEILEFF3 - 1765 - 178
16SERSERASPASPBB3 - 1775 - 179
26SERSERASPASPCC3 - 1775 - 179
17SERSERILEILEBB3 - 1765 - 178
27SERSERILEILEDD3 - 1765 - 178
18SERSERILEILEBB3 - 1765 - 178
28SERSERILEILEEE3 - 1765 - 178
19SERSERASPASPBB3 - 1775 - 179
29SERSERASPASPFF3 - 1775 - 179
110SERSERILEILECC3 - 1765 - 178
210SERSERILEILEDD3 - 1765 - 178
111SERSERILEILECC3 - 1765 - 178
211SERSERILEILEEE3 - 1765 - 178
112SERSERASPASPCC3 - 1775 - 179
212SERSERASPASPFF3 - 1775 - 179
113ASPASPILEILEDD2 - 1764 - 178
213ASPASPILEILEEE2 - 1764 - 178
114SERSERILEILEDD3 - 1765 - 178
214SERSERILEILEFF3 - 1765 - 178
115SERSERILEILEEE3 - 1765 - 178
215SERSERILEILEFF3 - 1765 - 178

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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.: 6 / Fragment: residues 22-198 / 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, 278 molecules

#2: Chemical
ChemComp-ZCM / CURIUM ION


Mass: 247.000 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cm
#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.: 6 / Source method: obtained synthetically / Formula: C34H38N8O12
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.14 Å3/Da / Density % sol: 60.77 %
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: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 56438 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.064 / Rrim(I) all: 0.15 / Χ2: 1.387 / Net I/av σ(I): 13.731 / Net I/σ(I): 7.6 / Num. measured all: 277210
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.4950.46328060.8760.2160.5130.692100
2.49-2.5450.42727940.8910.1980.4730.707100
2.54-2.5950.37527970.9140.1750.4150.72599.9
2.59-2.6450.35828510.9270.1660.3970.77399.8
2.64-2.750.32128250.9330.1490.3560.80499.9
2.7-2.7650.27527960.9480.1280.3040.85899.8
2.76-2.8350.24828200.9550.1160.2750.981100
2.83-2.950.23128390.960.1080.2561.08899.9
2.9-2.9950.20228080.9680.0940.2241.26799.6
2.99-3.094.90.17528040.9720.0820.1941.49899.3
3.09-3.24.90.16228350.9760.0760.181.55399.5
3.2-3.324.90.1428140.9840.0660.1561.89399.5
3.32-3.484.90.12928570.9850.0610.1431.9999.6
3.48-3.664.90.11628110.9860.0550.1292.18698.9
3.66-3.894.90.11128090.9870.0530.1242.20398.3
3.89-4.194.80.11128130.9850.0530.1242.10398.1
4.19-4.614.80.10628230.9810.0510.1181.76598
4.61-5.284.80.09528260.9890.0450.1051.38397
5.28-6.654.80.08428360.9930.0390.0931.52796.6
6.65-504.90.07728740.9950.0350.0851.85893.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
REFMAC5.8.0049phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHG

4zhg


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2132 / WRfactor Rwork: 0.193 / FOM work R set: 0.855 / SU B: 14.505 / SU ML: 0.164 / SU R Cruickshank DPI: 0.378 / SU Rfree: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2852 5.1 %RANDOM
Rwork0.2029 ---
obs0.2039 53541 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.5 Å2 / Biso mean: 29.413 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 404 252 9140
Biso mean--40.22 23.83 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.029208
X-RAY DIFFRACTIONr_bond_other_d0.0030.028523
X-RAY DIFFRACTIONr_angle_refined_deg0.9722.00312526
X-RAY DIFFRACTIONr_angle_other_deg0.731319630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8351077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54624.417412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.921151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8241539
X-RAY DIFFRACTIONr_chiral_restr0.0640.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110395
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022206
X-RAY DIFFRACTIONr_mcbond_it1.7021.4194245
X-RAY DIFFRACTIONr_mcbond_other1.6991.4194244
X-RAY DIFFRACTIONr_mcangle_it2.7522.125304
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102320.1
12B102320.1
21A101100.11
22C101100.11
31A105410.08
32D105410.08
41A100890.1
42E100890.1
51A102280.1
52F102280.1
61B105310.07
62C105310.07
71B102970.1
72D102970.1
81B100550.1
82E100550.1
91B103160.1
92F103160.1
101C100970.1
102D100970.1
111C99240.11
112E99240.11
121C101190.11
122F101190.11
131D100370.11
132E100370.11
141D100830.11
142F100830.11
151E103690.06
152F103690.06
LS refinement shellResolution: 2.45→2.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 213 -
Rwork0.256 3894 -
all-4107 -
obs--99.2 %
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)
10.525-0.9526-0.54592.63311.04321.8729-0.01060.02810.1678-0.14180.0412-0.4339-0.23670.1987-0.03060.1124-0.0301-0.00560.06740.02340.0902-16.2945-12.450628.9965
21.6042-1.41160.11492.08140.1010.9861-0.0475-0.14880.19090.26330.0991-0.2257-0.13010.1251-0.05170.1155-0.00990.01080.0602-0.00120.05624.2277-40.282413.7462
32.09510.5065-1.270.91270.62232.8144-0.06150.2211-0.1534-0.1082-0.04120.08160.2397-0.2530.10270.14620.0215-0.01060.0468-0.00340.1023-31.0478-42.867612.7751
40.5772-0.5044-1.00581.83751.16652.7118-0.00370.17510.0425-0.2246-0.01930.2182-0.2641-0.40420.02290.1208-0.0002-0.01250.08650.01850.1101-11.0575-56.7799-16.2682
51.8488-0.9945-0.13153.44630.09280.82230.11670.312-0.0967-0.395-0.067-0.11420.019-0.1098-0.04970.08740.00510.00160.0672-0.00580.09464.4559-31.0093-41.636
61.1440.28531.18690.87470.26073.22420.07320.1091-0.2916-0.04720.0065-0.18370.39880.0368-0.07960.0882-0.01490.0220.038-0.02640.115422.5928-69.0116-1.8479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2B3 - 301
3X-RAY DIFFRACTION3C3 - 301
4X-RAY DIFFRACTION4D2 - 301
5X-RAY DIFFRACTION5E2 - 301
6X-RAY DIFFRACTION6F3 - 301

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