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

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Basic information

Entry
Database: PDB / ID: 4zhh
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 / SAMARIUM (III) ION / Gene 8 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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

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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)130,83436
Polymers124,2036
Non-polymers6,63130
Water9,044502
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8256
Polymers20,7011
Non-polymers1,1255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7335
Polymers20,7011
Non-polymers1,0334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7696
Polymers20,7011
Non-polymers1,0685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9498
Polymers20,7011
Non-polymers1,2487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8256
Polymers20,7011
Non-polymers1,1255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7335
Polymers20,7011
Non-polymers1,0334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.683, 115.320, 120.517
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 176
2010B3 - 176
1020A3 - 176
2020C3 - 176
1030A2 - 176
2030D2 - 176
1040A2 - 176
2040E2 - 176
1050A3 - 176
2050F3 - 176
1060B3 - 177
2060C3 - 177
1070B3 - 176
2070D3 - 176
1080B3 - 176
2080E3 - 176
1090B3 - 177
2090F3 - 177
10100C3 - 176
20100D3 - 176
10110C3 - 176
20110E3 - 176
10120C3 - 177
20120F3 - 177
10130D2 - 177
20130E2 - 177
10140D3 - 176
20140F3 - 176
10150E3 - 176
20150F3 - 176

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 , 6 types, 532 molecules

#2: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sm
#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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
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: 5.0.1 / 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: 2.04→50 Å / Num. obs: 98255 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.071 / Χ2: 2.525 / Net I/av σ(I): 38.676 / Net I/σ(I): 16.9 / Num. measured all: 473803
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.04-2.084.60.20845641.56293.2
2.08-2.114.90.18949001.555100
2.11-2.154.90.16748781.596100
2.15-2.24.90.1649181.663100
2.2-2.2550.15248931.682100
2.25-2.34.90.13748651.80399.8
2.3-2.3550.12649321.887100
2.35-2.4250.11848981.96199.9
2.42-2.4950.10848762.068100
2.49-2.5750.10149722.184100
2.57-2.6650.09248652.24299.8
2.66-2.774.90.08549342.49399.9
2.77-2.894.90.07949172.61499.9
2.89-3.054.90.07149412.96699.8
3.05-3.244.90.06649403.25899.8
3.24-3.494.80.06349673.73899.5
3.49-3.844.60.06148974.1398.7
3.84-4.394.30.05649164.25498
4.39-5.544.50.05250083.92198.7
5.54-504.60.04651743.44998.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1759 / FOM work R set: 0.8874 / SU B: 4.96 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1492 / SU Rfree: 0.1312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 4899 5 %RANDOM
Rwork0.1743 ---
obs0.1755 93282 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 28.344 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8485 0 393 502 9380
Biso mean--29.08 29.5 -
Num. residues----1054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.029160
X-RAY DIFFRACTIONr_bond_other_d0.0040.028513
X-RAY DIFFRACTIONr_angle_refined_deg1.2472.00212448
X-RAY DIFFRACTIONr_angle_other_deg0.865319605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3524.425409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.117151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9871539
X-RAY DIFFRACTIONr_chiral_restr0.0840.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110333
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022190
X-RAY DIFFRACTIONr_mcbond_it2.1551.484230
X-RAY DIFFRACTIONr_mcbond_other2.1551.4794229
X-RAY DIFFRACTIONr_mcangle_it2.9872.25282
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101750.11
12B101750.11
21A100580.12
22C100580.12
31A105360.07
32D105360.07
41A101290.11
42E101290.11
51A101590.11
52F101590.11
61B103800.1
62C103800.1
71B102210.11
72D102210.11
81B100300.11
82E100300.11
91B102090.11
92F102090.11
101C100750.12
102D100750.12
111C98470.13
112E98470.13
121C100220.13
122F100220.13
131D100760.11
132E100760.11
141D101130.11
142F101130.11
151E105050.06
152F105050.06
LS refinement shellResolution: 2.04→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 328 -
Rwork0.186 6626 -
all-6954 -
obs--96.25 %
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)
11.5427-0.0887-0.39842.53610.59371.4927-0.01830.03440.1153-0.17080.0312-0.0948-0.12120.1021-0.01290.0392-0.0046-0.00980.01230.00010.0211-16.7115-11.768629.3551
21.6969-0.6148-0.31671.99620.27181.7718-0.0051-0.06690.05980.02610.0071-0.1346-0.03650.0979-0.0020.0095-0.00070.00180.00750.00030.01163.8007-38.74512.719
31.5477-0.0676-0.24571.75420.55432.74370.01570.0254-0.1211-0.0392-0.06820.1120.0723-0.21870.05250.0053-0.0051-0.00140.0178-0.00640.0195-31.3018-41.073712.8954
41.7418-0.1855-0.08151.50850.41972.6634-0.06710.1703-0.0292-0.0830.07270.0699-0.0872-0.0893-0.00550.0477-0.01830.01480.0402-0.02390.0541-11.7295-55.3066-16.2232
52.8832-0.59730.20822.1744-0.07252.44210.03580.0737-0.0989-0.1510.05720.0340.1854-0.1773-0.0930.0467-0.0329-0.02350.02830.01690.07396.6599-31.1446-42.0052
62.8416-0.89290.192.73870.0552.12870.23180.32330.0564-0.3723-0.2439-0.17690.027600.01210.11150.06290.01070.10330.03530.030121.2699-67.5788-2.672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 178
2X-RAY DIFFRACTION2B3 - 177
3X-RAY DIFFRACTION3C3 - 177
4X-RAY DIFFRACTION4D2 - 177
5X-RAY DIFFRACTION5E2 - 177
6X-RAY DIFFRACTION6F3 - 177

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