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Basic information

Entry
Database: PDB / ID: 6o5d
TitlePYOCHELIN
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / BETA-BARREL / SIDEROCALIN / ANTIMICROBIAL PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / enterobactin binding / iron ion sequestering activity / response to herbicide / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / Iron uptake and transport / acute-phase response / cellular response to nerve growth factor stimulus / response to virus / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / defense response to bacterium / iron ion binding / response to xenobiotic stimulus / innate immune response / Neutrophil degranulation / positive regulation of gene expression / 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
Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsRupert, P.B. / Strong, R.K. / Clifton, M.C. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Biol X / Year: 2019
Title: Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands.
Authors: Clifton, M.C. / Rupert, P.B. / Hoette, T.M. / Raymond, K.N. / Abergel, R.J. / Strong, R.K.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionSep 11, 2019ID: 3U03
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)61,04010
Polymers60,3753
Non-polymers6657
Water1,29772
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3173
Polymers20,1251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2212
Polymers20,1251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5015
Polymers20,1251
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.803, 114.803, 119.238
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 - 1772 - 173
21ASPASPASPASPBB6 - 1772 - 173
12SERSERILEILEAA5 - 1761 - 172
22SERSERILEILECC5 - 1761 - 172
13ASPASPASPASPBB6 - 1772 - 173
23ASPASPASPASPCC6 - 1772 - 173

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin / p25


Mass: 20125.037 Da / Num. of mol.: 3 / Fragment: residues 25-198 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pGex-4T / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P80188
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: HosaA.18070.a at 10 mg/ml. 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5. Cryoprotection 15% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30489 / % possible obs: 95.8 % / Redundancy: 8.4 % / Net I/σ(I): 29.8
Reflection shellResolution: 2.4→2.46 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 2.4→40.62 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.824 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.248
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 2900 9.5 %RANDOM
Rwork0.2326 ---
obs0.2347 27564 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 201.09 Å2 / Biso mean: 57.875 Å2 / Biso min: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 2.4→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4004 0 37 72 4113
Biso mean--83.01 39.06 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173697
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6495692
X-RAY DIFFRACTIONr_angle_other_deg1.2211.5718570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1235518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40123.333195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3451514
X-RAY DIFFRACTIONr_chiral_restr0.060.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A48170.07
12B48170.07
21A52320.08
22C52320.08
31B47820.06
32C47820.06
LS refinement shellResolution: 2.398→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 216 -
Rwork0.251 1968 -
all-2184 -
obs--96 %
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)
12.8223-0.63190.26794.93921.11862.15250.1980.2272-0.0069-0.1961-0.2463-0.1181-0.1534-0.26490.04820.09320.09770.03970.15420.00630.048528.84377.2154.587
22.8214-1.41610.80322.4609-0.04323.4344-0.0715-0.1523-0.0620.2619-0.07050.08970.0168-0.40010.1420.0890.01270.03480.0683-0.01570.112730.11368.14663.731
32.0219-1.3454-0.22073.12110.59561.52520.27230.27280.1484-0.1606-0.2792-0.1281-0.263-0.17440.00690.10660.08870.03690.11140.00960.070630.91876.9556.124
45.4551-2.4368-3.34542.1328-1.15779.8016-0.00180.2721-0.3898-0.22350.2320.30111.7152-0.8234-0.23021.3965-0.3337-0.41730.50880.02990.551853.38195.30936.779
54.9633-1.9966-0.84066.43590.59038.270.60950.79470.43760.3901-0.0108-0.40330.1813-0.2798-0.59870.4625-0.0689-0.21440.53350.07860.312853.606104.72727.683
64.5991-3.3865-0.35464.24870.51775.55640.85230.542-0.1721.0572-0.20290.28221.7827-0.9233-0.64942.1863-0.3736-0.38480.88170.2350.746651.0798.51936.745
73.5189-1.7202-0.62782.59580.44822.9178-0.10320.1077-0.0512-0.01560.0244-0.06720.12190.03790.07880.0214-0.0070.02090.01170.00020.039450.12349.3843.469
81.12470.14970.28021.53210.95575.9493-0.06450.0742-0.25780.07310.0820.08390.4824-0.3024-0.01750.0693-0.05940.00870.0847-0.03530.157940.0841.57142.42
92.014-0.09530.19231.3908-0.83942.31310.01640.1693-0.051-0.1552-0.071-0.04570.1370.03960.05460.0316-0.01080.02630.0454-0.0270.052249.49847.92741.564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 46
2X-RAY DIFFRACTION2A47 - 91
3X-RAY DIFFRACTION3A92 - 178
4X-RAY DIFFRACTION4B6 - 42
5X-RAY DIFFRACTION5B48 - 91
6X-RAY DIFFRACTION6B92 - 177
7X-RAY DIFFRACTION7C5 - 46
8X-RAY DIFFRACTION8C47 - 91
9X-RAY DIFFRACTION9C92 - 177

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