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- PDB-3fw5: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3fw5
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-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


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / 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 / iron ion sequestering activity / enterobactin binding / 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 / Neutrophil degranulation / apoptotic process / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / 4-METHYLCATECHOL / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / 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.ptnr1_label_seq_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

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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)63,23426
Polymers61,6693
Non-polymers1,56523
Water4,828268
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,11710
Polymers20,5561
Non-polymers5619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8294
Polymers20,5561
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,28912
Polymers20,5561
Non-polymers73211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.904, 114.904, 119.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-230-

HOH

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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, 291 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-MCT / 4-METHYLCATECHOL / 4-METHYL-1,2-BENZENEDIOL


Mass: 124.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 293 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 293K

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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: 67567 / Num. obs: 35984 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.39 / Num. unique all: 3519 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: Used previously-determined structure
Starting model: 1L6M

1l6m


Resolution: 2.3→40.62 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.761 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28973 3403 9.5 %RANDOM
Rwork0.24398 ---
obs0.24825 32519 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 92 268 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224154
X-RAY DIFFRACTIONr_bond_other_d0.0020.022813
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.975641
X-RAY DIFFRACTIONr_angle_other_deg0.7913.0026850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35624.251167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06915629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4781514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined0.1630.2642
X-RAY DIFFRACTIONr_nbd_other0.1810.22763
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21939
X-RAY DIFFRACTIONr_nbtor_other0.080.22270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.216
X-RAY DIFFRACTIONr_mcbond_it0.41822596
X-RAY DIFFRACTIONr_mcbond_other0.03821031
X-RAY DIFFRACTIONr_mcangle_it0.78434179
X-RAY DIFFRACTIONr_scbond_it0.75841617
X-RAY DIFFRACTIONr_scangle_it1.25761450
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 244 -
Rwork0.304 2320 -
obs--99.34 %

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