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- PDB-3by0: Crystal structure of Siderocalin (NGAL, Lipocalin 2) W79A-R81A co... -

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Basic information

Entry
Database: PDB / ID: 3by0
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) W79A-R81A complexed with Ferric Enterobactin
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsLIGAND BINDING PROTEIN / BETA BARREL
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
2,3-DIHYDROXY-BENZOIC ACID / Chem-DBS / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Used previously-determined structure / Resolution: 2.572 Å
AuthorsClifton, M.C. / Pizzaro, J.C. / Strong, R.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: The siderocalin/enterobactin interaction: a link between mammalian immunity and bacterial iron transport.
Authors: Abergel, R.J. / Clifton, M.C. / Pizarro, J.C. / Warner, J.A. / Shuh, D.K. / Strong, R.K. / Raymond, K.N.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 1.3Aug 30, 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)69,16618
Polymers67,1903
Non-polymers1,97615
Water1,40578
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1907
Polymers22,3971
Non-polymers7936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6073
Polymers22,3971
Non-polymers2102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3698
Polymers22,3971
Non-polymers9737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.358, 114.358, 119.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological subunit is a dimer, but dimerization was prevented by introducing a C87S mutation.

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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: 22396.715 Da / Num. of mol.: 3 / Mutation: W79A,R81A,C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: lcn2, ngal, hnl / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus RIL / References: UniProt: P80188

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Non-polymers , 6 types, 93 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DBS / 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID / 2,3,-DIHYDROXYBENZOYLSERINE


Type: L-peptide linking / Mass: 241.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11NO6
#5: Chemical
ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.572→28.59 Å / Num. all: 25655 / Num. obs: 23194 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 63.391 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 0.289
Reflection shellResolution: 2.572→2.66 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2519 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Used previously-determined structure
Starting model: PDB ENTRY 1L6M

1l6m


Resolution: 2.572→28.59 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.679 / SU ML: 0.212 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26249 2410 9.4 %Used same set as previously-determined structure
Rwork0.24751 ---
obs0.24891 23194 99.72 %-
all-25655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.572→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 126 78 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224424
X-RAY DIFFRACTIONr_bond_other_d0.0060.023023
X-RAY DIFFRACTIONr_angle_refined_deg0.841.9916000
X-RAY DIFFRACTIONr_angle_other_deg0.823.0027377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7955524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19524.627201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18615741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8431518
X-RAY DIFFRACTIONr_chiral_restr0.0530.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
X-RAY DIFFRACTIONr_nbd_refined0.1760.2540
X-RAY DIFFRACTIONr_nbd_other0.2070.22746
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21995
X-RAY DIFFRACTIONr_nbtor_other0.0780.22402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2130.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4561.52813
X-RAY DIFFRACTIONr_mcbond_other0.091.51037
X-RAY DIFFRACTIONr_mcangle_it0.58224254
X-RAY DIFFRACTIONr_scbond_it0.66832031
X-RAY DIFFRACTIONr_scangle_it0.9914.51741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.572→2.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 170 -
Rwork0.357 1603 -
obs-2519 96.36 %

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