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- PDB-1l6m: Neutrophil Gelatinase-associated Lipocalin is a Novel Bacteriosta... -

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Basic information

Entry
Database: PDB / ID: 1l6m
TitleNeutrophil Gelatinase-associated Lipocalin is a Novel Bacteriostatic Agent that Interferes with Siderophore-mediated Iron Acquisition
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / lipocalin / siderophore
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
2,3-DIHYDROXY-BENZOIC ACID / Chem-DBS / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGoetz, D.H. / Borregaard, N. / Bluhm, M.E. / Raymond, K.N. / Strong, R.K.
Citation
Journal: Mol.Cell / Year: 2002
Title: The Neutrophil Lipocalin NGAL is a Bacteriostatic Agent that Interferes with Siderophore-mediated Iron Acquisition
Authors: Goetz, D.H. / Borregaard, N. / Bluhm, M.E. / Raymond, K.N. / Strong, R.K.
#1: Journal: Biochemistry / Year: 2000
Title: Ligand preference inferred from the structure of Neutrophil Gelatinase Associated Lipocalin (NGAL)
Authors: Goetz, D.H. / Willie, S.T. / Armen, R. / Bratt, T. / Borregaard, N. / Strong, R.K.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet / 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_conn_type.id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,05217
Polymers62,1023
Non-polymers1,95014
Water1,09961
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4026
Polymers20,7011
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3065
Polymers20,7011
Non-polymers6054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3446
Polymers20,7011
Non-polymers6435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.078, 115.078, 115.221
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 / NGAL / P25 / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin 2 / Oncogene 24P3


Mass: 20700.564 Da / Num. of mol.: 3 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P80188

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Non-polymers , 5 types, 75 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H6O4
#5: Chemical ChemComp-DBS / 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID / 2,3,-DIHYDROXYBENZOYLSERINE


Type: L-peptide linking / Mass: 241.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11NO6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 298 K / pH: 7
Details: PEG 8000, ammonium sulphate, glycerol, PIPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.00
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion / Details: Goetz, D.H., (2000) Biochemistry, 39, 1935.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
218-22 %(w/w)PEG80001reservoir
315 %(v/v)glycerol1reservoir
4100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→19.76 Å / Num. obs: 29626 / % possible obs: 96.5 % / Rsym value: 0.057
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 30746 / % possible obs: 100 % / Num. measured all: 312664 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 100 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
EPMRphasing
REFMAC5refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QQS

1qqs


Resolution: 2.4→19.76 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.133 / SU ML: 0.192 / Isotropic thermal model: ISOTROPIC AND TLS / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.25818 1470 5 %RANDOM
Rwork0.23248 ---
obs0.23376 28156 96.52 %-
all-30746 --
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: 38.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 124 61 4318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.985940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7283521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.522752
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023366
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.31880
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.5375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.346
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.52591
X-RAY DIFFRACTIONr_mcangle_it1.91124211
X-RAY DIFFRACTIONr_scbond_it2.11331775
X-RAY DIFFRACTIONr_scangle_it3.584.51729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 92
Rwork0.284 1797
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)
10.6871-0.655-0.17511.38280.35480.59050.09470.0709-0.01450.0038-0.0548-0.1416-0.134-0.0447-0.03990.1453-0.01260.00680.10970.0180.131630.190874.519555.6796
21.9681-0.2905-0.01611.83540.35082.70180.1320.15170.04620.2454-0.1-0.02980.1854-0.3565-0.0320.121-0.03720.0140.14730.03420.012554.399197.676333.8195
31.6079-0.80920.26450.51820.01980.65340.09050.20230.15080.0475-0.1569-0.10410.0893-0.0560.06650.0867-0.00890.03580.15980.04810.161146.961246.08240.3138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1776 - 179
2X-RAY DIFFRACTION1AD - L200 - 2031
3X-RAY DIFFRACTION2BB4 - 1776 - 179
4X-RAY DIFFRACTION2BE - O300 - 3031
5X-RAY DIFFRACTION3CC5 - 1777 - 179
6X-RAY DIFFRACTION3CF - Q400 - 4031
Refinement
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å / Rfactor Rfree: 0.359 / Rfactor Rwork: 0.25

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