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

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Basic information

Entry
Database: PDB / ID: 3cmp
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsANTIMICROBIAL PROTEIN / Lipocalin / Siderocalin / Enterobactin / Siderophore / Iron / 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
2,3-DIHYDROXY-BENZOIC ACID / Chem-EB4 / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsClifton, M.C. / Strong, R.K.
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
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Oct 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 1.4Aug 30, 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.end_auth_comp_id
Revision 1.5Nov 13, 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)70,16023
Polymers67,6203
Non-polymers2,54020
Water1,67593
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5727
Polymers22,5401
Non-polymers1,0336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9275
Polymers22,5401
Non-polymers3874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,66011
Polymers22,5401
Non-polymers1,12110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.908, 114.908, 118.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
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: 4 / Auth seq-ID: 5 - 177 / Label seq-ID: 25 - 197

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC
DetailsC87S mutation disrupts dimer formation

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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: 22539.861 Da / Num. of mol.: 3 / Mutation: C87S, K125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3+RIL / References: UniProt: P80188

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Non-polymers , 7 types, 113 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin


Mass: 669.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O15
#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: Chemical ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M Ammonium sulfate, 30% PEG4000, 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
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→82.48 Å / Num. all: 20269 / Num. obs: 20066 / % possible obs: 99 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.85
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.92 / Num. unique all: 1955 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L6M

1l6m


Resolution: 2.8→47.96 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.823 / SU B: 15.276 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R: 0.947 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30397 1026 5.1 %Used same set as previously-determined structure
Rwork0.24827 ---
obs0.25108 19017 99.02 %-
all-20269 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 161 93 4165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224173
X-RAY DIFFRACTIONr_bond_other_d0.0070.022715
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.9915685
X-RAY DIFFRACTIONr_angle_other_deg0.7923.0026617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07424.294163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1451513
X-RAY DIFFRACTIONr_chiral_restr0.0560.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_nbd_refined0.1680.2704
X-RAY DIFFRACTIONr_nbd_other0.180.22654
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22036
X-RAY DIFFRACTIONr_nbtor_other0.0780.22119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1250.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.23
X-RAY DIFFRACTIONr_mcbond_it0.28622575
X-RAY DIFFRACTIONr_mcbond_other0.0321026
X-RAY DIFFRACTIONr_mcangle_it0.54134130
X-RAY DIFFRACTIONr_scbond_it0.52941654
X-RAY DIFFRACTIONr_scangle_it0.88561554
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2255 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.132
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 88 -
Rwork0.391 1347 -
obs--99.1 %

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