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- PDB-3s26: Crystal Structure of Murine Siderocalin (Lipocalin 2, 24p3) -

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Basic information

Entry
Database: PDB / ID: 3s26
TitleCrystal Structure of Murine Siderocalin (Lipocalin 2, 24p3)
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / Beta-Barrel / Siderophore binding protein / N-Linked glycosylation / Secreted
Function / homology
Function and homology information


positive regulation of hippocampal neuron apoptotic process / Metal sequestration by antimicrobial proteins / positive regulation of iron ion import across plasma membrane / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / cytoplasmic vesicle lumen / Iron uptake and transport / siderophore transport / short-term memory ...positive regulation of hippocampal neuron apoptotic process / Metal sequestration by antimicrobial proteins / positive regulation of iron ion import across plasma membrane / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / cytoplasmic vesicle lumen / Iron uptake and transport / siderophore transport / short-term memory / iron ion sequestering activity / enterobactin binding / response to herbicide / positive regulation of reactive oxygen species biosynthetic process / small molecule binding / long-term memory / extrinsic apoptotic signaling pathway in absence of ligand / Neutrophil degranulation / positive regulation of endothelial cell migration / response to bacterium / response to virus / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / protease binding / defense response to bacterium / response to xenobiotic stimulus / iron ion binding / positive regulation of apoptotic process / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol
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
Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCorrenti, C. / Bandaranayake, A.D. / Strong, R.K.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Daedalus: a robust, turnkey platform for rapid production of decigram quantities of active recombinant proteins in human cell lines using novel lentiviral vectors.
Authors: Bandaranayake, A.D. / Correnti, C. / Ryu, B.Y. / Brault, M. / Strong, R.K. / Rawlings, D.J.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8452
Polymers22,0971
Non-polymers7491
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 43.960, 101.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / Lipocalin-2 / SV-40-induced 24P3 protein / p25


Mass: 22096.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lcn2 / Cell line (production host): HEK293F / Production host: Homo Sapiens (human) / References: UniProt: P11672
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20% PEG 4000, 10% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 315r / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.89 Å / Num. all: 18585 / Num. obs: 18574 / % possible obs: 99.9 % / Redundancy: 6.87 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.867.090.4263.51100
1.86-1.947.080.3064.61100
1.94-2.037.070.226.21100
2.03-2.137.010.1678199.9
2.13-2.276.980.12810.11100
2.27-2.446.970.10511.9199.8
2.44-2.696.870.07715.11100
2.69-3.086.780.06918.7199.9
3.08-3.886.540.04826.2199.9
3.88-42.896.390.0343.2199.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ddata reduction
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.329 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22605 948 5.1 %RANDOM
Rwork0.20085 ---
obs0.20216 17592 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 50 89 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221428
X-RAY DIFFRACTIONr_bond_other_d0.0010.02964
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9861942
X-RAY DIFFRACTIONr_angle_other_deg0.82932327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60222.95161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.979159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9932842
X-RAY DIFFRACTIONr_mcbond_other0.6382337
X-RAY DIFFRACTIONr_mcangle_it3.21331363
X-RAY DIFFRACTIONr_scbond_it4.2114586
X-RAY DIFFRACTIONr_scangle_it6.3266579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 65 -
Rwork0.236 1297 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 1.7609 Å / Origin y: -2.677 Å / Origin z: -12.488 Å
111213212223313233
T0.1696 Å20.0313 Å20.0104 Å2-0.1847 Å20.0263 Å2--0.1844 Å2
L1.2884 °20.7274 °20.592 °2-1.6022 °2-0.0189 °2--1.8132 °2
S0.0236 Å °0.1097 Å °0.0991 Å °0.0988 Å °-0.0018 Å °0.027 Å °0.0376 Å °0.0787 Å °-0.0218 Å °

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