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- PDB-3fw4: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3fw4
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric Catechol
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / 8-stranded anti-parallel beta barrel / 310-helix / Glycoprotein / Pyrrolidone carboxylic acid / Secreted
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 / iron ion sequestering activity / enterobactin binding / 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 / acute-phase response / Iron uptake and transport / 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
CATECHOL / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsClifton, M.C. / Strong, R.K.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.
Authors: Bao, G. / Clifton, M. / Hoette, T.M. / Mori, K. / Deng, S.X. / Qiu, A. / Viltard, M. / Williams, D. / Paragas, N. / Leete, T. / Kulkarni, R. / Li, X. / Lee, B. / Kalandadze, A. / Ratner, A.J. ...Authors: Bao, G. / Clifton, M. / Hoette, T.M. / Mori, K. / Deng, S.X. / Qiu, A. / Viltard, M. / Williams, D. / Paragas, N. / Leete, T. / Kulkarni, R. / Li, X. / Lee, B. / Kalandadze, A. / Ratner, A.J. / Pizarro, J.C. / Schmidt-Ott, K.M. / Landry, D.W. / Raymond, K.N. / Strong, R.K. / Barasch, J.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)63,49233
Polymers61,6693
Non-polymers1,82230
Water4,378243
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,22213
Polymers20,5561
Non-polymers66512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6834
Polymers20,5561
Non-polymers1273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,58716
Polymers20,5561
Non-polymers1,03015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.421, 115.421, 118.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 20556.438 Da / Num. of mol.: 3 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL / References: UniProt: P80188

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Non-polymers , 6 types, 273 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.0-1.4M Ammonium sulfate, 50 mM Sodium Chloride, 200 mM Lithium Sulfate, 100 mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 210 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 68321 / Num. obs: 36375 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.09 / Num. unique all: 3562 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementStarting model: 1L6M

1l6m


Resolution: 2.3→40.79 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.721 / SU ML: 0.168
Isotropic thermal model: Used previously-determined structure
Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28376 3443 9.5 %RANDOM
Rwork0.25562 ---
obs0.25827 32869 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 99 243 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223884
X-RAY DIFFRACTIONr_bond_other_d0.0020.022618
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9695258
X-RAY DIFFRACTIONr_angle_other_deg0.8223.0026369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95724.276152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8771513
X-RAY DIFFRACTIONr_chiral_restr0.0630.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.1650.2663
X-RAY DIFFRACTIONr_nbd_other0.1760.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21843
X-RAY DIFFRACTIONr_nbtor_other0.0780.22032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1180.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it0.36622458
X-RAY DIFFRACTIONr_mcbond_other0.0342979
X-RAY DIFFRACTIONr_mcangle_it0.69433919
X-RAY DIFFRACTIONr_scbond_it0.74741483
X-RAY DIFFRACTIONr_scangle_it1.24761332
LS refinement shellResolution: 2.297→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 252 -
Rwork0.303 2348 -
obs--98.93 %

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