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

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Basic information

Entry
Database: PDB / ID: 3hwg
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / Lipocalin / siderophore / beta-barrel / Disulfide bond / Glycoprotein / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule 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 / 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 / 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
: / Chem-QED / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.19 Å
AuthorsClifton, M.C.
CitationJournal: To be Published
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
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.4Sep 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

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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)71,62837
Polymers67,7943
Non-polymers3,83434
Water3,009167
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,05115
Polymers22,5981
Non-polymers1,45314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3985
Polymers22,5981
Non-polymers8014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,17817
Polymers22,5981
Non-polymers1,58116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.084, 114.084, 118.422
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-191-

NA

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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: 22597.963 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) / References: UniProt: P80188

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Non-polymers , 7 types, 201 molecules

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


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-QED / N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2 -carboxamide) / tren mono-2,3-catecholamido bis-N-hydroxypyridin-2-one-6-amide


Mass: 556.525 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H28N6O9
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 52918 / Num. obs: 40660 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 24.29
Reflection shellResolution: 2.19→2.28 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.6 / Num. unique all: 3989 / % possible all: 100

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Processing

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

1l6m


Resolution: 2.19→46.93 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.553 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26785 3868 9.5 %Used same set as previously-determined structure
Rwork0.24244 ---
obs0.24482 36725 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.19→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 239 167 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224380
X-RAY DIFFRACTIONr_bond_other_d0.0010.022969
X-RAY DIFFRACTIONr_angle_refined_deg1.0382.0045943
X-RAY DIFFRACTIONr_angle_other_deg0.7663.0027227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0735524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57723.953172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9815665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8841515
X-RAY DIFFRACTIONr_chiral_restr0.0550.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214768
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02911
X-RAY DIFFRACTIONr_mcbond_it0.42422600
X-RAY DIFFRACTIONr_mcbond_other0.04121031
X-RAY DIFFRACTIONr_mcangle_it0.79834210
X-RAY DIFFRACTIONr_scbond_it0.75741780
X-RAY DIFFRACTIONr_scangle_it1.31261726
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 287 -
Rwork0.277 2589 -
obs--97.56 %

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