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- PDB-3ped: Siderocalin Recognitin of Carboxymycobactins: Interference by the... -

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Basic information

Entry
Database: PDB / ID: 3ped
TitleSiderocalin Recognitin of Carboxymycobactins: Interference by the immune system in intracellular iron acquisition by Mycobacteria tuberculosis
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsANTIMICROBIAL PROTEIN / 8-stranded anti-parallel beta barrel / Siderocalin / Siderophore binding
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / enterobactin binding / iron ion sequestering activity / 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 / enterobactin binding / iron ion sequestering activity / 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 / 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
: / Chem-ZYF / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.3 Å
AuthorsClifton, M.C.
CitationJournal: To be Published
Title: Siderocalin Recognitin of Carboxymycobactins: Interference by the immune system in intracellular iron acquisition by Mycobacteria tuberculosis
Authors: Hoette, T.M. / Clifton, M.C. / Zawadzka, A.M. / Holmes, M.A. / Strong, R.K. / Raymond, K.R.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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 1.2Oct 30, 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)64,21210
Polymers61,6693
Non-polymers2,5437
Water2,864159
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3723
Polymers20,5561
Non-polymers8162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3723
Polymers20,5561
Non-polymers8162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4684
Polymers20,5561
Non-polymers9123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.200, 114.200, 119.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 20556.438 Da / Num. of mol.: 3 / Fragment: UNP residues 21 to 198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZYF / (9Z)-11-{hydroxy[(5S)-6-{[(1S)-3-{[(3S)-1-hydroxy-2-oxoazepan-3-yl]amino}-1-methyl-3-oxopropyl]oxy}-5-({[(4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)-6-oxohexyl]amino}-11-oxoundec-9-enoic acid


Mass: 759.843 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H53N5O12
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 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 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 66620 / Num. obs: 35471 / % possible obs: 99.8 %
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.5 / Num. unique all: 3502 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: Used previously-determined structure
Starting model: PDB entry 1L6M

1l6m


Resolution: 2.3→48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.56 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24317 3359 9.5 %RANDOM
Rwork0.20415 ---
obs0.2078 32071 99.85 %-
all-35471 --
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: 41.839 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 170 159 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224378
X-RAY DIFFRACTIONr_bond_other_d0.0010.022999
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9965949
X-RAY DIFFRACTIONr_angle_other_deg0.83137346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35323.851161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9691514
X-RAY DIFFRACTIONr_chiral_restr0.0450.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02892
X-RAY DIFFRACTIONr_mcbond_it0.5771.52625
X-RAY DIFFRACTIONr_mcbond_other0.0851.51040
X-RAY DIFFRACTIONr_mcangle_it1.07624268
X-RAY DIFFRACTIONr_scbond_it1.31331753
X-RAY DIFFRACTIONr_scangle_it2.1834.51675
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 230 -
Rwork0.231 2174 -
obs--99.71 %

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