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- PDB-3tzs: Crystal structure of Neutrophil gelatinase-associated lipocalin N... -

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Basic information

Entry
Database: PDB / ID: 3tzs
TitleCrystal structure of Neutrophil gelatinase-associated lipocalin NGAL (C87S mutant) in complex with fragment 1026, phenylurea
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsAPOPTOSIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / iron trafficking / lipocalin / siderocalin / fragment based drug design / FBDD / Fragments of Life / EBSI-01644
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
1-phenylurea / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
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
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 13, 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 / 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 1.4Oct 9, 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)64,80621
Polymers63,1263
Non-polymers1,68018
Water2,846158
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6047
Polymers21,0421
Non-polymers5626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4065
Polymers21,0421
Non-polymers3644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7969
Polymers21,0421
Non-polymers7548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.350, 115.350, 119.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / p25


Mass: 21041.971 Da / Num. of mol.: 3 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL, Oncogene 24p3 / Production host: Escherichia coli (E. coli) / References: UniProt: P80188

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Non-polymers , 5 types, 176 molecules

#2: Chemical
ChemComp-PHU / 1-phenylurea / Phenylurea


Mass: 136.151 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8N2O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: HosaA.18070.a protein at 10 mg/mL against 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate with 15% glycerol as cryo-protectant, crystal tracking ID ...Details: HosaA.18070.a protein at 10 mg/mL against 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate with 15% glycerol as cryo-protectant, crystal tracking ID 224571a10, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 30343 / Num. obs: 30248 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 37.733 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.45-2.516.40.5433.64141262193218999.8
2.51-2.580.4644.24137772141100
2.58-2.660.4044.7813414208799.7
2.66-2.740.345.6113035204599.9
2.74-2.830.2776.6912462194899.8
2.83-2.930.2347.5912346193299.9
2.93-3.040.1849.4311580182599.8
3.04-3.160.15510.6211340179299.9
3.16-3.30.13112.1510589169799.7
3.3-3.460.11213.8410214165199.8
3.46-3.650.09915.969551155299.7
3.65-3.870.09316.469066148699.7
3.87-4.140.08518.088451140099.8
4.14-4.470.0819.27818129999.7
4.47-4.90.07620.267277121799.8
4.9-5.480.07819.616578111399.9
5.48-6.330.08118.7577598499.4
6.33-7.750.07819.02484683499.4
7.75-10.960.07120.64377666998.7
10.960.0719.95201738793.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TF6

3tf6


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2252 / WRfactor Rwork: 0.1859 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8533 / SU B: 12.681 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2902 / SU Rfree: 0.2184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1532 5.1 %RANDOM
Rwork0.1872 ---
obs0.1891 30248 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.53 Å2 / Biso mean: 31.3309 Å2 / Biso min: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 101 158 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024302
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9755859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03124.162185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05715662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1631517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213298
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 109 -
Rwork0.241 1882 -
all-1991 -
obs--99.75 %
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)
12.1324-0.5351-0.2413.691.00881.35060.1195-0.04210.0197-0.2066-0.0429-0.2455-0.1458-0.0479-0.07660.03490.02470.01790.03910.01040.017829.512877.605655.5509
21.9363-0.75580.76911.4960.34640.66270.0112-0.1654-0.0420.26220.001-0.03950.1301-0.1079-0.01220.09320.0025-0.0350.03060.00750.084133.0767.887665.5201
30.7951-0.37810.01162.08160.20840.75990.13090.1080.009-0.0344-0.084-0.1033-0.1131-0.0789-0.0470.06420.03890.0170.0352-0.00070.039729.549776.35257.2111
40.9810.23090.14252.47841.51913.87760.146-0.00950.00830.1251-0.22340.30250.1849-0.27320.07740.0328-0.02350.0170.0515-0.04150.060253.773395.407736.0987
53.7324-3.7001-0.15613.89190.71191.4170.17690.27750.2235-0.2926-0.2683-0.1967-0.3647-0.06910.09140.23650.0845-0.05180.1069-0.01190.117751.8764105.868625.947
61.09230.09210.4331.31030.13682.60450.1511-0.07610.03630.086-0.15670.0360.1487-0.14730.00570.0298-0.02280.00150.0419-0.02530.042154.227697.065135.5333
72.8396-1.2689-0.55281.92660.27441.5024-0.02150.15830.1923-0.1361-0.0655-0.12920.0303-0.03320.08710.03190.0140.01650.0250.02120.03349.620749.676242.9026
80.47850.04540.61251.30140.73621.50340.0492-0.0428-0.1363-0.0022-0.095-0.00590.0389-0.35820.04580.0413-0.0197-0.02170.1911-0.11160.166838.752240.716640.061
91.0249-0.11120.08530.5358-0.42760.98210.01790.05740.0504-0.0249-0.0616-0.06440.05830.05890.04370.0350.0107-0.00180.04330.02780.047848.561947.691643.2504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 47
2X-RAY DIFFRACTION2A48 - 79
3X-RAY DIFFRACTION3A80 - 177
4X-RAY DIFFRACTION4B5 - 48
5X-RAY DIFFRACTION5B49 - 81
6X-RAY DIFFRACTION6B82 - 177
7X-RAY DIFFRACTION7C5 - 48
8X-RAY DIFFRACTION8C49 - 79
9X-RAY DIFFRACTION9C80 - 177

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