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

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Basic information

Entry
Database: PDB / ID: 3pec
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 / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule 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 / 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 / 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
: / Chem-ZYG / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.19 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,48619
Polymers61,6693
Non-polymers1,81616
Water4,107228
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0216
Polymers20,5561
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin


Theoretical massNumber of molelcules
Total (without water)20,5561
Polymers20,5561
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)21,90812
Polymers20,5561
Non-polymers1,35211
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

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 6 types, 244 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ZYG / 9-{hydroxy[(5S,6R)-6-hydroxy-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)hexyl]amino}-9-oxononanoic acid


Mass: 735.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H53N5O12
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 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: 2.2→50 Å / Num. all: 77333 / Num. obs: 41091 / % possible obs: 100 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4024 / % 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: 2.19→40.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.636 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27294 3912 9.5 %RANDOM
Rwork0.24522 ---
obs0.24783 37100 99.95 %-
all-41091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.19→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 114 228 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224276
X-RAY DIFFRACTIONr_bond_other_d0.0010.022899
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9745816
X-RAY DIFFRACTIONr_angle_other_deg0.863.0027080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7175531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3624.389180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03215654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6091514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_mcbond_it0.1861.52611
X-RAY DIFFRACTIONr_mcbond_other0.0221.51037
X-RAY DIFFRACTIONr_mcangle_it0.35924226
X-RAY DIFFRACTIONr_scbond_it0.46331665
X-RAY DIFFRACTIONr_scangle_it0.8284.51581
LS refinement shellResolution: 2.186→2.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 269 -
Rwork0.286 2362 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2447-0.8922-0.08974.5540.68651.02550.16030.1137-0.0663-0.0883-0.20420.1105-0.0353-0.19820.04390.08020.06710.03350.1343-0.00660.041126.778775.074453.6913
21.4508-1.69510.32571.9945-0.50792.5343-0.07820.02620.16540.16310.0173-0.1945-0.0212-0.03990.06090.15560.04740.0060.0651-0.01380.176534.475871.371264.3437
33.0422-2.8331.41823.8019-0.37043.463-0.1223-0.21480.05470.3606-0.12610.1849-0.1029-0.22350.24850.0986-0.05370.0420.1936-0.01150.176820.795570.003163.7461
42.408-1.601-0.72143.05250.64310.88630.06220.01140.0160.0111-0.02330.0666-0.0468-0.0369-0.0390.08990.05930.01270.1424-0.00480.108227.134775.723557.0648
51.736-1.01870.1512.1026-0.45832.71960.24780.35360.2078-0.2664-0.2142-0.5113-0.09780.1439-0.03360.11370.03320.08020.09830.00960.170838.311478.552352.6233
63.0386-1.5975-0.92565.87641.85442.64750.18390.3130.04460.282-0.258-0.17050.4152-0.10350.07410.1718-0.11160.02540.2774-0.01290.014456.853691.270433.4623
71.107-1.89830.57567.89812.76843.5641-0.04940.22460.2791-0.3702-0.3807-0.0991-0.5599-0.16820.43010.13030.0364-0.05040.49350.14880.121651.0038103.744228.8104
86.85314.9055-0.859.91624.52324.22180.14920.767-0.01570.09550.7063-1.1562-0.02140.0043-0.85550.144-0.1195-0.15730.31810.09930.376765.686299.862529.8483
94.4945-0.1323-0.2653.60582.43962.28080.0679-0.01450.11720.2714-0.16950.12140.0478-0.44770.10150.2592-0.0825-0.05820.2740.02870.028555.923296.892935.5794
100.8258-1.858-0.83545.24393.70254.4993-0.496-0.1353-0.29881.1273-0.22591.03950.5375-1.29310.72190.3210.04130.15410.76750.07110.329344.876394.486938.7608
112.6502-0.8463-0.44921.5011-0.02732.1587-0.0333-0.06540.0025-0.0067-0.0046-0.00930.058-0.0320.03790.0932-0.01690.00140.04810.0060.095647.454450.313545.7218
120.80110.20881.15092.2624-0.04132.2310.00190.1376-0.1519-0.1514-0.018-0.05860.22430.03350.01610.1476-0.07740.01880.1303-0.06330.21241.841440.671837.6853
131.539-0.19110.1141.2681-0.771.67050.00360.0491-0.0269-0.1139-0.0233-0.0110.11330.01930.01970.1029-0.00760.00880.1064-0.02120.110247.70747.593245.2201
144.52521.68612.52672.88680.63743.1382-0.20610.38120.23-0.4319-0.04870.01450.07910.10760.25480.14720.02090.04510.1226-0.00960.060749.408646.899332.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 38
2X-RAY DIFFRACTION2A39 - 77
3X-RAY DIFFRACTION3A78 - 100
4X-RAY DIFFRACTION4A101 - 143
5X-RAY DIFFRACTION5A144 - 178
6X-RAY DIFFRACTION6B6 - 34
7X-RAY DIFFRACTION7B35 - 80
8X-RAY DIFFRACTION8B81 - 99
9X-RAY DIFFRACTION9B100 - 145
10X-RAY DIFFRACTION10B146 - 177
11X-RAY DIFFRACTION11C4 - 39
12X-RAY DIFFRACTION12C40 - 78
13X-RAY DIFFRACTION13C79 - 157
14X-RAY DIFFRACTION14C158 - 178

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