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- PDB-3u0d: The structure of human Siderocalin bound to the bacterial siderop... -

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Basic information

Entry
Database: PDB / ID: 3u0d
TitleThe structure of human Siderocalin bound to the bacterial siderophore 2,3-DHBA
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsANTIMICROBIAL PROTEIN / siderophore / beta-barrel / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSPORT PROTEIN
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin 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 ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin 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 / Neutrophil degranulation / apoptotic process / 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
2,3-DIHYDROXY-BENZOIC ACID / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2012
Title: Siderocalin/Lcn2/NGAL/24p3 does not drive apoptosis through gentisic acid mediated iron withdrawal in hematopoietic cell lines.
Authors: Correnti, C. / Richardson, V. / Sia, A.K. / Bandaranayake, A.D. / Ruiz, M. / Suryo Rahmanto, Y. / Kovacevic, Z. / Clifton, M.C. / Holmes, M.A. / Kaiser, B.K. / Barasch, J. / Raymond, K.N. / ...Authors: Correnti, C. / Richardson, V. / Sia, A.K. / Bandaranayake, A.D. / Ruiz, M. / Suryo Rahmanto, Y. / Kovacevic, Z. / Clifton, M.C. / Holmes, M.A. / Kaiser, B.K. / Barasch, J. / Raymond, K.N. / Richardson, D.R. / Strong, R.K.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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 / 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_seq_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_auth_seq_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_auth_seq_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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57123
Polymers90,3924
Non-polymers2,17919
Water3,315184
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1526
Polymers22,5981
Non-polymers5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1526
Polymers22,5981
Non-polymers5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1165
Polymers22,5981
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1526
Polymers22,5981
Non-polymers5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.476, 116.452, 120.194
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsC107S mutant forces monomer

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Components

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


Mass: 22597.963 Da / Num. of mol.: 4 / Mutation: C107S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3+RIL / References: UniProt: P80188
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H6O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 4.55 Å3/Da / Density % sol: 72.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: HosaA.18070.a at 10mg/ml. 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5. Cryo protection 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Sep 1, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.428
11K, H, -L20.572
ReflectionResolution: 2.5→50 Å / Num. obs: 55324 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.118 / Χ2: 1.027 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.546.20.47927571199.7
2.54-2.596.20.40927531.04199.8
2.59-2.646.20.37827721.093199.6
2.64-2.696.20.33527441.095199.5
2.69-2.756.20.28127491.086199.5
2.75-2.826.20.23827981.053199.4
2.82-2.896.20.22527211.085199.3
2.89-2.966.20.18627771.091199.4
2.96-3.056.20.15827511.033199.2
3.05-3.156.20.14627430.994198.7
3.15-3.266.20.13227710.975199.1
3.26-3.396.20.11927820.961199
3.39-3.556.20.11127320.973198.5
3.55-3.736.20.11127601.014198.3
3.73-3.976.20.10527760.983198.4
3.97-4.276.20.1127481.079197.8
4.27-4.76.20.11827541.031197.9
4.7-5.386.10.11427751.027197.1
5.38-6.7860.08827930.948196.5
6.78-506.10.07528680.972194.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.51 Å42.01 Å
Translation2.51 Å42.01 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6M

1l6m


Resolution: 2.51→42.01 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.3074 / WRfactor Rwork: 0.2604 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7615 / SU B: 13.648 / SU ML: 0.156 / SU R Cruickshank DPI: 0.0639 / SU Rfree: 0.0541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 5498 9.9 %RANDOM
Rwork0.2469 ---
obs0.251 55279 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.97 Å2 / Biso mean: 41.7926 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å20 Å2
2--3.6 Å20 Å2
3----7.17 Å2
Refinement stepCycle: LAST / Resolution: 2.51→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 139 184 5873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025845
X-RAY DIFFRACTIONr_bond_other_d0.0010.023914
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9847947
X-RAY DIFFRACTIONr_angle_other_deg0.9573.0029541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93724.574258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64915939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8211520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021212
LS refinement shellResolution: 2.512→2.577 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 352 -
Rwork0.285 2906 -
all-3258 -
obs--78.64 %
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)
15.41141.9357-0.25851.6337-0.91060.82770.00530.2139-0.0634-0.109-0.0441-0.08970.0130.18860.03880.1959-0.00620.03240.13950.02890.150928.39597.4253-4.4102
21.2912-0.5005-0.64461.0749-0.0112.1838-0.0036-0.13390.10790.06990.00160.0846-0.0964-0.18040.00190.17310.0179-0.01040.1055-0.02320.204212.911714.2834.2774
31.61680.3109-0.57231.9497-0.74421.48790.0074-0.00010.01660.0247-0.0335-0.0081-0.04810.03350.02620.1830.0108-0.03140.1138-0.01250.154819.388511.9649-2.1981
40.76360.4129-1.11541.6639-0.55671.994-0.1244-0.1755-0.13110.0528-0.113-0.06130.01080.08660.23730.17610.0398-0.03540.17870.01930.167222.88025.840411.0686
55.5676-0.1969-0.42533.4211-1.87953.4987-0.27270.2379-0.24810.0470.24290.1339-0.0990.01610.02980.22770.02720.07590.13260.04670.211716.7224-4.9241-27.4144
61.3985-0.15220.08551.3303-0.19272.28830.01810.07810.1048-0.1067-0.08810.1132-0.1806-0.10280.070.14860.02120.00110.0791-0.01020.166816.760915.7495-32.9009
72.79470.7407-1.20391.793-0.8662.39920.0165-0.09210.020.0818-0.02730.02010.0382-0.02790.01080.19510.0146-0.02090.065-0.03640.115417.261910.8804-25.2149
81.6594-0.0245-0.35271.3627-0.47131.4759-0.04440.062-0.0666-0.1752-0.1143-0.00140.09620.04440.15870.19720.00520.00450.0693-0.04960.134821.7936.2188-38.3163
91.76250.5906-0.4393.70120.36750.90280.2216-0.08880.11690.1422-0.24030.00890.0122-0.14110.01870.2373-0.0751-0.03280.1615-0.0340.147-0.9758-18.8462-9.2058
101.93390.8888-0.59951.5418-0.29973.11410.11380.12220.0271-0.0884-0.10920.12790.0059-0.3817-0.00460.2357-0.0221-0.00790.1205-0.00390.2065-0.0891-12.4825-19.5787
112.52341.04620.42592.6180.22751.15380.197-0.1253-0.00620.0348-0.16240.00970.0099-0.0816-0.03460.2324-0.06510.01760.1233-0.00750.16890.1586-18.7143-10.4936
122.07711.4869-0.44553.0366-1.60721.94280.1657-0.255-0.30760.1106-0.3428-0.6415-0.065-0.00270.17710.2423-0.077-0.02370.15850.02330.23969.3602-22.6106-9.5495
138.6648-0.84245.93093.39320.551610.3239-0.1378-0.06980.08520.04430.25950.0374-0.1283-0.4443-0.12180.2627-0.1760.04870.3249-0.04570.275961.174534.4514-19.2797
142.21560.5403-0.84222.33870.14941.0875-0.21220.0567-0.17230.01760.22080.0637-0.0406-0.0289-0.00860.2776-0.08160.00640.1823-0.01430.18945.360425.7115-19.6573
151.12790.5026-0.29431.282-0.89172.3395-0.1552-0.05110.12780.14480.18140.1659-0.4398-0.1014-0.02620.23920.0163-0.00570.16520.01130.227540.379230.4427-10.8862
162.32680.88070.09591.59990.10580.7785-0.14660.1448-0.1256-0.12470.1505-0.0746-0.1280.0719-0.00390.1864-0.07350.00980.10870.00340.151749.279625.6132-19.4508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 21
2X-RAY DIFFRACTION2A22 - 86
3X-RAY DIFFRACTION3A87 - 143
4X-RAY DIFFRACTION4A144 - 178
5X-RAY DIFFRACTION5B3 - 15
6X-RAY DIFFRACTION6B16 - 87
7X-RAY DIFFRACTION7B88 - 127
8X-RAY DIFFRACTION8B128 - 177
9X-RAY DIFFRACTION9C5 - 43
10X-RAY DIFFRACTION10C44 - 101
11X-RAY DIFFRACTION11C102 - 149
12X-RAY DIFFRACTION12C150 - 178
13X-RAY DIFFRACTION13D5 - 15
14X-RAY DIFFRACTION14D16 - 48
15X-RAY DIFFRACTION15D49 - 99
16X-RAY DIFFRACTION16D100 - 178

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