[English] 日本語
Yorodumi
- PDB-4zhh: Siderocalin-mediated recognition and cellular uptake of actinides -

+
Open data


ID or keywords:

Loading...

-
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


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-4OL / SAMARIUM (III) ION / Neutrophil gelatinase-associated lipocalin
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
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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:

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
13ASPASPILEILEAA2 - 1764 - 178
23ASPASPILEILEDD2 - 1764 - 178
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
113ASPASPASPASPDD2 - 1774 - 179
213ASPASPASPASPEE2 - 1774 - 179
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more