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- PDB-3hwd: Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A-K134A ... -

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Basic information

Entry
Database: PDB / ID: 3hwd
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) K125A-K134A mutant complexed with Ferric Enterobactin
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / Lipocalin / siderophore / beta-barrel / Disulfide bond / 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
Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.95 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 / Category: database_2 / 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_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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,60610
Polymers67,4453
Non-polymers1617
Water91951
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5052
Polymers22,4821
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin


Theoretical massNumber of molelcules
Total (without water)22,4821
Polymers22,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6207
Polymers22,4821
Non-polymers1386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.825, 115.825, 119.316
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-184-

NA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 5 - 177 / Label seq-ID: 25 - 197

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC

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Components

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


Mass: 22481.760 Da / Num. of mol.: 3 / Mutation: C87S, K125A, K134A
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
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M lithium sulfate, 20% PEG 3350, 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: 2.95→50 Å / Num. all: 29078 / Num. obs: 16029 / % possible obs: 91 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 2.95→3.1 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1613 / % possible all: 93.7

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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: 2.95→50 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.829 / SU B: 16.57 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30292 808 5 %Used same set as previously-determined structure
Rwork0.25727 ---
obs0.2595 15193 90.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.763 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 7 51 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223968
X-RAY DIFFRACTIONr_bond_other_d0.0010.022606
X-RAY DIFFRACTIONr_angle_refined_deg0.8291.9545406
X-RAY DIFFRACTIONr_angle_other_deg0.7923.0026342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4095505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2923.851161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9711514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_nbd_refined0.1670.2629
X-RAY DIFFRACTIONr_nbd_other0.1730.22464
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21886
X-RAY DIFFRACTIONr_nbtor_other0.0770.22140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1230.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.24
X-RAY DIFFRACTIONr_mcbond_it0.34522556
X-RAY DIFFRACTIONr_mcbond_other0.03321016
X-RAY DIFFRACTIONr_mcangle_it0.64534079
X-RAY DIFFRACTIONr_scbond_it0.50141461
X-RAY DIFFRACTIONr_scangle_it0.85661327
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1017tight positional0.020.05
1224loose positional0.565
1017tight thermal0.030.5
1224loose thermal0.4710
LS refinement shellResolution: 2.953→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 62 -
Rwork0.317 1103 -
obs--91.23 %

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